[
  {
    "metric_id": "BEMO:2000001",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000001",
    "preferred_label": "Biological Gradient",
    "normalized_label": "biological_gradient",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100001",
    "category_label": "Biological Plausibility and Mechanism",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100001",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of biological gradient.",
    "what_it_measures": "Assesses biological gradient using evidence appropriate to biological plausibility and mechanism, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in biological gradient can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "related_frameworks_source": "GRADE; FDA Biomarker; ClinGen; OHAT; OECD",
    "closely_related_metrics_source": "Off-Target Liability Evidence; Homeostatic Compensation Assessment; Network Context Support",
    "common_misinterpretations": "Treating biological gradient as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "domain_applicability": "Biological Plausibility and Mechanism",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000001",
    "api_endpoint_template": "/v1/metrics/BEMO:2000001/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000001_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 8,
    "source_record_hash": "6471dcf670c9dd05424f4606389decf6b51812d07c0a0680842d77bda957b0f3",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 8; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000002",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000002",
    "preferred_label": "Biological Plausibility",
    "normalized_label": "biological_plausibility",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100001",
    "category_label": "Biological Plausibility and Mechanism",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100001",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of biological plausibility.",
    "what_it_measures": "Assesses biological plausibility using evidence appropriate to biological plausibility and mechanism, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in biological plausibility can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "related_frameworks_source": "GRADE; FDA Biomarker; ClinGen; OHAT; OECD",
    "closely_related_metrics_source": "Mechanistic Support; Mechanistic Coverage",
    "common_misinterpretations": "Treating biological plausibility as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "domain_applicability": "Biological Plausibility and Mechanism",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000002",
    "api_endpoint_template": "/v1/metrics/BEMO:2000002/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000002_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 9,
    "source_record_hash": "6cbc5f525d668cebb0928b8428848a625103a7b6492d0a2a618adb116f200bd3",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 9; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000003",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000003",
    "preferred_label": "Cell-Type Specificity",
    "normalized_label": "cell_type_specificity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100001",
    "category_label": "Biological Plausibility and Mechanism",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100001",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of cell-type specificity.",
    "what_it_measures": "Assesses cell-type specificity using evidence appropriate to biological plausibility and mechanism, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in cell-type specificity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified threshold; valid reference standard; complete 2×2 classification; confidence intervals; spectrum and prevalence assessment.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "related_frameworks_source": "GRADE; FDA Biomarker; ClinGen; OHAT; OECD",
    "closely_related_metrics_source": "Pathway-Level Support; Tissue Specificity; Spatial Biological Concordance",
    "common_misinterpretations": "Treating cell-type specificity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "domain_applicability": "Biological Plausibility and Mechanism",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000003",
    "api_endpoint_template": "/v1/metrics/BEMO:2000003/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000003_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 10,
    "source_record_hash": "8fcb10135485d0dff26bef51519f2178a09a543c766f354a728ca79b2c39c582",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 10; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000004",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000004",
    "preferred_label": "Cross-Species Biological Concordance",
    "normalized_label": "cross_species_biological_concordance",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100001",
    "category_label": "Biological Plausibility and Mechanism",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100001",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree of agreement in cross-species biological across measurements, studies, methods, populations, or biological levels.",
    "what_it_measures": "Assesses cross-species biological concordance using evidence appropriate to biological plausibility and mechanism, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in cross-species biological concordance can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "related_frameworks_source": "GRADE; FDA Biomarker; ClinGen; OHAT; OECD",
    "closely_related_metrics_source": "Temporal Biological Concordance; Phenotypic Concordance; Molecular-Phenotypic Concordance",
    "common_misinterpretations": "Treating cross-species biological concordance as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "domain_applicability": "Biological Plausibility and Mechanism",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000004",
    "api_endpoint_template": "/v1/metrics/BEMO:2000004/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000004_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 11,
    "source_record_hash": "6f883b8ebe7aa3d7407688c8b2390b245a894c21f5c21ffef99fe634674c5fd3",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 11; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000005",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000005",
    "preferred_label": "Epistasis Support",
    "normalized_label": "epistasis_support",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100001",
    "category_label": "Biological Plausibility and Mechanism",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100001",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting epistasis.",
    "what_it_measures": "Assesses epistasis support using evidence appropriate to biological plausibility and mechanism, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in epistasis support can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "related_frameworks_source": "GRADE; FDA Biomarker; ClinGen; OHAT; OECD",
    "closely_related_metrics_source": "Rescue Experiment Support; Target Engagement Evidence; On-Target Specificity",
    "common_misinterpretations": "Treating epistasis support as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "domain_applicability": "Biological Plausibility and Mechanism",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000005",
    "api_endpoint_template": "/v1/metrics/BEMO:2000005/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000005_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 12,
    "source_record_hash": "cd57f610728234561644257a8387987f0aa8934688593c5fbd817b3779032054",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 12; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000006",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000006",
    "preferred_label": "Gain-of-Function Validation",
    "normalized_label": "gain_of_function_validation",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100001",
    "category_label": "Biological Plausibility and Mechanism",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100001",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of gain-of-function validation.",
    "what_it_measures": "Assesses gain-of-function validation using evidence appropriate to biological plausibility and mechanism, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in gain-of-function validation can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "related_frameworks_source": "GRADE; FDA Biomarker; ClinGen; OHAT; OECD",
    "closely_related_metrics_source": "Loss-of-Function Validation; Rescue Experiment Support; Epistasis Support",
    "common_misinterpretations": "Treating gain-of-function validation as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "domain_applicability": "Biological Plausibility and Mechanism",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000006",
    "api_endpoint_template": "/v1/metrics/BEMO:2000006/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000006_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 13,
    "source_record_hash": "5c02cfac370a9d2c1514479546d6e291e60bffe1758412ceec02bbf8edaab2dc",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 13; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000007",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000007",
    "preferred_label": "Homeostatic Compensation Assessment",
    "normalized_label": "homeostatic_compensation_assessment",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100001",
    "category_label": "Biological Plausibility and Mechanism",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100001",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of homeostatic compensation assessment.",
    "what_it_measures": "Assesses homeostatic compensation assessment using evidence appropriate to biological plausibility and mechanism, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in homeostatic compensation assessment can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "related_frameworks_source": "GRADE; FDA Biomarker; ClinGen; OHAT; OECD",
    "closely_related_metrics_source": "Biological Gradient; Network Context Support; Systems-Level Emergence Support",
    "common_misinterpretations": "Treating homeostatic compensation assessment as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "domain_applicability": "Biological Plausibility and Mechanism",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000007",
    "api_endpoint_template": "/v1/metrics/BEMO:2000007/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000007_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 14,
    "source_record_hash": "61aaa3d7ba71760f01fcbbb79304031b61f416940944ef459f48b6d07dc0628d",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 14; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000008",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000008",
    "preferred_label": "Loss-of-Function Validation",
    "normalized_label": "loss_of_function_validation",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100001",
    "category_label": "Biological Plausibility and Mechanism",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100001",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of loss-of-function validation.",
    "what_it_measures": "Assesses loss-of-function validation using evidence appropriate to biological plausibility and mechanism, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in loss-of-function validation can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "related_frameworks_source": "GRADE; FDA Biomarker; ClinGen; OHAT; OECD",
    "closely_related_metrics_source": "Perturbational Validation; Gain-of-Function Validation; Rescue Experiment Support",
    "common_misinterpretations": "Treating loss-of-function validation as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "domain_applicability": "Biological Plausibility and Mechanism",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000008",
    "api_endpoint_template": "/v1/metrics/BEMO:2000008/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000008_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 15,
    "source_record_hash": "7b09e166eefa32f832c89264de2b3521f93b540fbc674d78fc625fd792779d09",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 15; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000009",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000009",
    "preferred_label": "Mechanistic Causality Strength",
    "normalized_label": "mechanistic_causality_strength",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100001",
    "category_label": "Biological Plausibility and Mechanism",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100001",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting mechanistic causality.",
    "what_it_measures": "Assesses mechanistic causality strength using evidence appropriate to biological plausibility and mechanism, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in mechanistic causality strength can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Directed acyclic graphs; design emulation; balance diagnostics; negative controls; quantitative bias analysis; sensitivity and falsification analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "related_frameworks_source": "GRADE; FDA Biomarker; ClinGen; OHAT; OECD",
    "closely_related_metrics_source": "Mechanistic Specificity; Pathway-Level Support; Cell-Type Specificity",
    "common_misinterpretations": "Treating mechanistic causality strength as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "domain_applicability": "Biological Plausibility and Mechanism",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000009",
    "api_endpoint_template": "/v1/metrics/BEMO:2000009/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000009_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 16,
    "source_record_hash": "114851a566f6667271761fd50b701ab810f623c4ee0ecdabe88d5bbacc5941db",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 16; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000010",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000010",
    "preferred_label": "Mechanistic Coherence",
    "normalized_label": "mechanistic_coherence",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100001",
    "category_label": "Biological Plausibility and Mechanism",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100001",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of mechanistic coherence.",
    "what_it_measures": "Assesses mechanistic coherence using evidence appropriate to biological plausibility and mechanism, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in mechanistic coherence can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "related_frameworks_source": "GRADE; FDA Biomarker; ClinGen; OHAT; OECD",
    "closely_related_metrics_source": "Mechanistic Completeness; Mechanistic Specificity; Mechanistic Causality Strength",
    "common_misinterpretations": "Treating mechanistic coherence as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "domain_applicability": "Biological Plausibility and Mechanism",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000010",
    "api_endpoint_template": "/v1/metrics/BEMO:2000010/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000010_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 17,
    "source_record_hash": "dc1b3b375698d0aec42693d5a0b2f87405e7e7bf90759105797ad714ab4e9ab2",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 17; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000011",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000011",
    "preferred_label": "Mechanistic Completeness",
    "normalized_label": "mechanistic_completeness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100001",
    "category_label": "Biological Plausibility and Mechanism",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100001",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which all scientifically necessary components of mechanistic are present, documented, and evaluable.",
    "what_it_measures": "Assesses mechanistic completeness using evidence appropriate to biological plausibility and mechanism, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in mechanistic completeness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "related_frameworks_source": "GRADE; FDA Biomarker; ClinGen; OHAT; OECD",
    "closely_related_metrics_source": "Mechanistic Coverage; Mechanistic Coherence; Mechanistic Specificity",
    "common_misinterpretations": "Treating mechanistic completeness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "domain_applicability": "Biological Plausibility and Mechanism",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000011",
    "api_endpoint_template": "/v1/metrics/BEMO:2000011/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000011_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 18,
    "source_record_hash": "70dc43fe10f07fb6cf3546a825ad424f5db2e21cc1b19a9f92b47d758bf660bd",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 18; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000012",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000012",
    "preferred_label": "Mechanistic Coverage",
    "normalized_label": "mechanistic_coverage",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100001",
    "category_label": "Biological Plausibility and Mechanism",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100001",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The proportion and representativeness of the relevant mechanistic captured by the evidence or measurement process.",
    "what_it_measures": "Assesses mechanistic coverage using evidence appropriate to biological plausibility and mechanism, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in mechanistic coverage can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "related_frameworks_source": "GRADE; FDA Biomarker; ClinGen; OHAT; OECD",
    "closely_related_metrics_source": "Mechanistic Support; Mechanistic Completeness; Mechanistic Coherence",
    "common_misinterpretations": "Treating mechanistic coverage as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "domain_applicability": "Biological Plausibility and Mechanism",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000012",
    "api_endpoint_template": "/v1/metrics/BEMO:2000012/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000012_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 19,
    "source_record_hash": "8582aac321a237f1dd1db68f0893021d3bc987b71b373d1879cc2dfb098adbdb",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 19; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000013",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000013",
    "preferred_label": "Mechanistic Specificity",
    "normalized_label": "mechanistic_specificity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100001",
    "category_label": "Biological Plausibility and Mechanism",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100001",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of mechanistic specificity.",
    "what_it_measures": "Assesses mechanistic specificity using evidence appropriate to biological plausibility and mechanism, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in mechanistic specificity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified threshold; valid reference standard; complete 2×2 classification; confidence intervals; spectrum and prevalence assessment.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "related_frameworks_source": "GRADE; FDA Biomarker; ClinGen; OHAT; OECD",
    "closely_related_metrics_source": "Mechanistic Coherence; Mechanistic Causality Strength; Pathway-Level Support",
    "common_misinterpretations": "Treating mechanistic specificity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "domain_applicability": "Biological Plausibility and Mechanism",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000013",
    "api_endpoint_template": "/v1/metrics/BEMO:2000013/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000013_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 20,
    "source_record_hash": "29074cf2dac765628d0a639b922f2e3313846aa414af9c4ef760ea93c86819ca",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 20; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000014",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000014",
    "preferred_label": "Mechanistic Support",
    "normalized_label": "mechanistic_support",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100001",
    "category_label": "Biological Plausibility and Mechanism",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100001",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting mechanistic.",
    "what_it_measures": "Assesses mechanistic support using evidence appropriate to biological plausibility and mechanism, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in mechanistic support can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "related_frameworks_source": "GRADE; FDA Biomarker; ClinGen; OHAT; OECD",
    "closely_related_metrics_source": "Biological Plausibility; Mechanistic Coverage; Mechanistic Completeness",
    "common_misinterpretations": "Treating mechanistic support as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "domain_applicability": "Biological Plausibility and Mechanism",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000014",
    "api_endpoint_template": "/v1/metrics/BEMO:2000014/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000014_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 21,
    "source_record_hash": "d05eb179325de1077bb0eedc4d22a5f8c9cc2049d4ca5a5830b380984606cc90",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 21; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000015",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000015",
    "preferred_label": "Molecular-Phenotypic Concordance",
    "normalized_label": "molecular_phenotypic_concordance",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100001",
    "category_label": "Biological Plausibility and Mechanism",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100001",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree of agreement in molecular-phenotypic across measurements, studies, methods, populations, or biological levels.",
    "what_it_measures": "Assesses molecular-phenotypic concordance using evidence appropriate to biological plausibility and mechanism, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in molecular-phenotypic concordance can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "related_frameworks_source": "GRADE; FDA Biomarker; ClinGen; OHAT; OECD",
    "closely_related_metrics_source": "Phenotypic Concordance; Perturbational Validation; Loss-of-Function Validation",
    "common_misinterpretations": "Treating molecular-phenotypic concordance as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "domain_applicability": "Biological Plausibility and Mechanism",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000015",
    "api_endpoint_template": "/v1/metrics/BEMO:2000015/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000015_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 22,
    "source_record_hash": "81a78e88eaa62f6e2bb0ae947aba28fe819150032abcf9264f9205803cc7dfd1",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 22; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000016",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000016",
    "preferred_label": "Network Context Support",
    "normalized_label": "network_context_support",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100001",
    "category_label": "Biological Plausibility and Mechanism",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100001",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting network context.",
    "what_it_measures": "Assesses network context support using evidence appropriate to biological plausibility and mechanism, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in network context support can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "related_frameworks_source": "GRADE; FDA Biomarker; ClinGen; OHAT; OECD",
    "closely_related_metrics_source": "Homeostatic Compensation Assessment; Systems-Level Emergence Support",
    "common_misinterpretations": "Treating network context support as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "domain_applicability": "Biological Plausibility and Mechanism",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000016",
    "api_endpoint_template": "/v1/metrics/BEMO:2000016/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000016_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 23,
    "source_record_hash": "d14cae7a1ae4e812a18da95395619423ade3837794dc32beea80cb11af0003f0",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 23; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000017",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000017",
    "preferred_label": "Off-Target Liability Evidence",
    "normalized_label": "off_target_liability_evidence",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100001",
    "category_label": "Biological Plausibility and Mechanism",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100001",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of off-target liability evidence.",
    "what_it_measures": "Assesses off-target liability evidence using evidence appropriate to biological plausibility and mechanism, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in off-target liability evidence can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "related_frameworks_source": "GRADE; FDA Biomarker; ClinGen; OHAT; OECD",
    "closely_related_metrics_source": "On-Target Specificity; Biological Gradient; Homeostatic Compensation Assessment",
    "common_misinterpretations": "Treating off-target liability evidence as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "domain_applicability": "Biological Plausibility and Mechanism",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000017",
    "api_endpoint_template": "/v1/metrics/BEMO:2000017/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000017_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 24,
    "source_record_hash": "688a2bdbd29ad4b59eca6350cf3462f2bc158ee3d70ef4de59f338b6e6c797a6",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 24; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000018",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000018",
    "preferred_label": "On-Target Specificity",
    "normalized_label": "on_target_specificity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100001",
    "category_label": "Biological Plausibility and Mechanism",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100001",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of on-target specificity.",
    "what_it_measures": "Assesses on-target specificity using evidence appropriate to biological plausibility and mechanism, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in on-target specificity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified threshold; valid reference standard; complete 2×2 classification; confidence intervals; spectrum and prevalence assessment.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "related_frameworks_source": "GRADE; FDA Biomarker; ClinGen; OHAT; OECD",
    "closely_related_metrics_source": "Target Engagement Evidence; Off-Target Liability Evidence; Biological Gradient",
    "common_misinterpretations": "Treating on-target specificity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "domain_applicability": "Biological Plausibility and Mechanism",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000018",
    "api_endpoint_template": "/v1/metrics/BEMO:2000018/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000018_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 25,
    "source_record_hash": "5b75004715c78ae57eb0dfbf1a6fe3b6212289ca6b06f39e35b36270d16b13e5",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 25; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000019",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000019",
    "preferred_label": "Pathway-Level Support",
    "normalized_label": "pathway_level_support",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100001",
    "category_label": "Biological Plausibility and Mechanism",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100001",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting pathway-level.",
    "what_it_measures": "Assesses pathway-level support using evidence appropriate to biological plausibility and mechanism, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in pathway-level support can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "related_frameworks_source": "GRADE; FDA Biomarker; ClinGen; OHAT; OECD",
    "closely_related_metrics_source": "Mechanistic Causality Strength; Cell-Type Specificity; Tissue Specificity",
    "common_misinterpretations": "Treating pathway-level support as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "domain_applicability": "Biological Plausibility and Mechanism",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000019",
    "api_endpoint_template": "/v1/metrics/BEMO:2000019/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000019_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 26,
    "source_record_hash": "a1a0e0a377d9f949a45a0ad0a040b0443e29f24bfe701f3b015420b52cd21ab2",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 26; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000020",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000020",
    "preferred_label": "Perturbational Validation",
    "normalized_label": "perturbational_validation",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100001",
    "category_label": "Biological Plausibility and Mechanism",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100001",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of perturbational validation.",
    "what_it_measures": "Assesses perturbational validation using evidence appropriate to biological plausibility and mechanism, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in perturbational validation can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "related_frameworks_source": "GRADE; FDA Biomarker; ClinGen; OHAT; OECD",
    "closely_related_metrics_source": "Molecular-Phenotypic Concordance; Loss-of-Function Validation; Gain-of-Function Validation",
    "common_misinterpretations": "Treating perturbational validation as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "domain_applicability": "Biological Plausibility and Mechanism",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000020",
    "api_endpoint_template": "/v1/metrics/BEMO:2000020/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000020_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 27,
    "source_record_hash": "e56c259480c9a3f5c7efe467a62a9721824469292b9aeb900d1804f2bbfb7983",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 27; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000021",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000021",
    "preferred_label": "Phenotypic Concordance",
    "normalized_label": "phenotypic_concordance",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100001",
    "category_label": "Biological Plausibility and Mechanism",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100001",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree of agreement in phenotypic across measurements, studies, methods, populations, or biological levels.",
    "what_it_measures": "Assesses phenotypic concordance using evidence appropriate to biological plausibility and mechanism, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in phenotypic concordance can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "related_frameworks_source": "GRADE; FDA Biomarker; ClinGen; OHAT; OECD",
    "closely_related_metrics_source": "Cross-Species Biological Concordance; Molecular-Phenotypic Concordance; Perturbational Validation",
    "common_misinterpretations": "Treating phenotypic concordance as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "domain_applicability": "Biological Plausibility and Mechanism",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000021",
    "api_endpoint_template": "/v1/metrics/BEMO:2000021/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000021_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 28,
    "source_record_hash": "d6b2622e1418a4a4c75dd4e74edee6d3fe7ea5ecac7eb6c453c614421e29173a",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 28; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000022",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000022",
    "preferred_label": "Rescue Experiment Support",
    "normalized_label": "rescue_experiment_support",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100001",
    "category_label": "Biological Plausibility and Mechanism",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100001",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting rescue experiment.",
    "what_it_measures": "Assesses rescue experiment support using evidence appropriate to biological plausibility and mechanism, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in rescue experiment support can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "related_frameworks_source": "GRADE; FDA Biomarker; ClinGen; OHAT; OECD",
    "closely_related_metrics_source": "Gain-of-Function Validation; Epistasis Support; Target Engagement Evidence",
    "common_misinterpretations": "Treating rescue experiment support as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "domain_applicability": "Biological Plausibility and Mechanism",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000022",
    "api_endpoint_template": "/v1/metrics/BEMO:2000022/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000022_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 29,
    "source_record_hash": "9f3de30fb4252544b664477f26ad879c47cffd18e4a902652a07ca5b9fa59ec2",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 29; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000023",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000023",
    "preferred_label": "Spatial Biological Concordance",
    "normalized_label": "spatial_biological_concordance",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100001",
    "category_label": "Biological Plausibility and Mechanism",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100001",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree of agreement in spatial biological across measurements, studies, methods, populations, or biological levels.",
    "what_it_measures": "Assesses spatial biological concordance using evidence appropriate to biological plausibility and mechanism, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in spatial biological concordance can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "related_frameworks_source": "GRADE; FDA Biomarker; ClinGen; OHAT; OECD",
    "closely_related_metrics_source": "Tissue Specificity; Temporal Biological Concordance; Cross-Species Biological Concordance",
    "common_misinterpretations": "Treating spatial biological concordance as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "domain_applicability": "Biological Plausibility and Mechanism",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000023",
    "api_endpoint_template": "/v1/metrics/BEMO:2000023/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000023_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 30,
    "source_record_hash": "6c08ba26b1257f37b62212d7633a9e83166a0f74706ae3ffbb9de90cd98613f7",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 30; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000024",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000024",
    "preferred_label": "Systems-Level Emergence Support",
    "normalized_label": "systems_level_emergence_support",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100001",
    "category_label": "Biological Plausibility and Mechanism",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100001",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting systems-level emergence.",
    "what_it_measures": "Assesses systems-level emergence support using evidence appropriate to biological plausibility and mechanism, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in systems-level emergence support can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "related_frameworks_source": "GRADE; FDA Biomarker; ClinGen; OHAT; OECD",
    "closely_related_metrics_source": "Network Context Support",
    "common_misinterpretations": "Treating systems-level emergence support as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "domain_applicability": "Biological Plausibility and Mechanism",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000024",
    "api_endpoint_template": "/v1/metrics/BEMO:2000024/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000024_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 31,
    "source_record_hash": "07df8f6070c405006e36806e8ccb515126dc2c7269ea9cf3934662d28e9264c6",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 31; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000025",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000025",
    "preferred_label": "Target Engagement Evidence",
    "normalized_label": "target_engagement_evidence",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100001",
    "category_label": "Biological Plausibility and Mechanism",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100001",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of target engagement evidence.",
    "what_it_measures": "Assesses target engagement evidence using evidence appropriate to biological plausibility and mechanism, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in target engagement evidence can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "related_frameworks_source": "GRADE; FDA Biomarker; ClinGen; OHAT; OECD",
    "closely_related_metrics_source": "Epistasis Support; On-Target Specificity; Off-Target Liability Evidence",
    "common_misinterpretations": "Treating target engagement evidence as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "domain_applicability": "Biological Plausibility and Mechanism",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000025",
    "api_endpoint_template": "/v1/metrics/BEMO:2000025/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000025_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 32,
    "source_record_hash": "a51c69d24f2bf9ef711f1d3b54d2086032245754bf1992c1b5999a88e3ca185f",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 32; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000026",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000026",
    "preferred_label": "Temporal Biological Concordance",
    "normalized_label": "temporal_biological_concordance",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100001",
    "category_label": "Biological Plausibility and Mechanism",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100001",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree of agreement in temporal biological across measurements, studies, methods, populations, or biological levels.",
    "what_it_measures": "Assesses temporal biological concordance using evidence appropriate to biological plausibility and mechanism, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in temporal biological concordance can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "related_frameworks_source": "GRADE; FDA Biomarker; ClinGen; OHAT; OECD",
    "closely_related_metrics_source": "Spatial Biological Concordance; Cross-Species Biological Concordance; Phenotypic Concordance",
    "common_misinterpretations": "Treating temporal biological concordance as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "domain_applicability": "Biological Plausibility and Mechanism",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000026",
    "api_endpoint_template": "/v1/metrics/BEMO:2000026/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000026_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 33,
    "source_record_hash": "57d68c3c49543e85a4a6ee1a26a1705e9e0e05df169673d5a8f0a00632bfa39b",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 33; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000027",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000027",
    "preferred_label": "Tissue Specificity",
    "normalized_label": "tissue_specificity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100001",
    "category_label": "Biological Plausibility and Mechanism",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100001",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of tissue specificity.",
    "what_it_measures": "Assesses tissue specificity using evidence appropriate to biological plausibility and mechanism, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in tissue specificity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified threshold; valid reference standard; complete 2×2 classification; confidence intervals; spectrum and prevalence assessment.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "related_frameworks_source": "GRADE; FDA Biomarker; ClinGen; OHAT; OECD",
    "closely_related_metrics_source": "Cell-Type Specificity; Spatial Biological Concordance; Temporal Biological Concordance",
    "common_misinterpretations": "Treating tissue specificity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Molecular, cellular, animal, translational, pharmacologic, and human studies",
    "domain_applicability": "Biological Plausibility and Mechanism",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000027",
    "api_endpoint_template": "/v1/metrics/BEMO:2000027/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000027_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 34,
    "source_record_hash": "e3cc6b49f3bcbfabd500e6222a7c3cc053aca55c824a6afddd04a9b448378651",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 34; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.fda.gov/media/119271/download | https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000028",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000028",
    "preferred_label": "Biomarker Clinical Relevance",
    "normalized_label": "biomarker_clinical_relevance",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of biomarker clinical relevance.",
    "what_it_measures": "Assesses biomarker clinical relevance using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in biomarker clinical relevance can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Biomarker-Outcome Association Strength; Context-of-Use Validity; Biomarker Qualification Strength",
    "common_misinterpretations": "Treating biomarker clinical relevance as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000028",
    "api_endpoint_template": "/v1/metrics/BEMO:2000028/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000028_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 35,
    "source_record_hash": "70bbbca5f05350dbfed193659c18ff0eef66a6552528618a931911c0bbfe7878",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 35; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000029",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000029",
    "preferred_label": "Biomarker Qualification Strength",
    "normalized_label": "biomarker_qualification_strength",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting biomarker qualification.",
    "what_it_measures": "Assesses biomarker qualification strength using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in biomarker qualification strength can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Context-of-Use Validity; Biomarker Reliability; Biomarker Responsiveness",
    "common_misinterpretations": "Treating biomarker qualification strength as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000029",
    "api_endpoint_template": "/v1/metrics/BEMO:2000029/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000029_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 36,
    "source_record_hash": "35003a5d4be2844c7914597bb95d8d44ce388ce934a6b5067c8e498ac9e8de35",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 36; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000030",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000030",
    "preferred_label": "Biomarker Reliability",
    "normalized_label": "biomarker_reliability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of biomarker reliability.",
    "what_it_measures": "Assesses biomarker reliability using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in biomarker reliability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Biomarker Qualification Strength; Biomarker Responsiveness; Biomarker Sensitivity to Change",
    "common_misinterpretations": "Treating biomarker reliability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000030",
    "api_endpoint_template": "/v1/metrics/BEMO:2000030/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000030_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 37,
    "source_record_hash": "74c0c7f33ecc210cbe2fa1dd5ddc15c31273005f3e5caaa4afc370a3f6c94a4e",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 37; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000031",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000031",
    "preferred_label": "Biomarker Responsiveness",
    "normalized_label": "biomarker_responsiveness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of biomarker responsiveness.",
    "what_it_measures": "Assesses biomarker responsiveness using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in biomarker responsiveness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Biomarker Reliability; Biomarker Sensitivity to Change; Known-Groups Validity",
    "common_misinterpretations": "Treating biomarker responsiveness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000031",
    "api_endpoint_template": "/v1/metrics/BEMO:2000031/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000031_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 38,
    "source_record_hash": "19a54854b5dfb7168eddad304da95ddbab2e1ad34992146fcedfd650dfe09548",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 38; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000032",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000032",
    "preferred_label": "Biomarker Sensitivity to Change",
    "normalized_label": "biomarker_sensitivity_to_change",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of biomarker sensitivity to change.",
    "what_it_measures": "Assesses biomarker sensitivity to change using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in biomarker sensitivity to change can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified threshold; valid reference standard; complete 2×2 classification; confidence intervals; spectrum and prevalence assessment.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Biomarker Responsiveness; Known-Groups Validity; Convergent Validity",
    "common_misinterpretations": "Treating biomarker sensitivity to change as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000032",
    "api_endpoint_template": "/v1/metrics/BEMO:2000032/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000032_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 39,
    "source_record_hash": "80beed232e03f65da1843b394120d8baef7fb4428401374caac926260837e2b2",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 39; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000033",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000033",
    "preferred_label": "Biomarker-Outcome Association Strength",
    "normalized_label": "biomarker_outcome_association_strength",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting biomarker-outcome association.",
    "what_it_measures": "Assesses biomarker-outcome association strength using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in biomarker-outcome association strength can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Clinical Validity; Biomarker Clinical Relevance; Context-of-Use Validity",
    "common_misinterpretations": "Treating biomarker-outcome association strength as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000033",
    "api_endpoint_template": "/v1/metrics/BEMO:2000033/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000033_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 40,
    "source_record_hash": "d54499df144e3534026302c035690746b731c0abf25107f5fccdd8bada0bd79a",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 40; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000034",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000034",
    "preferred_label": "Clinical Validity",
    "normalized_label": "clinical_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which clinical supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses clinical validity using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in clinical validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Biomarker-Outcome Association Strength; Biomarker Clinical Relevance",
    "common_misinterpretations": "Treating clinical validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000034",
    "api_endpoint_template": "/v1/metrics/BEMO:2000034/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000034_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 41,
    "source_record_hash": "628005d99d3e18a7b100ce400c64fc5218e46beeaa2cfec80dbac2445270cead",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 41; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000035",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000035",
    "preferred_label": "Construct Validity",
    "normalized_label": "construct_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which construct supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses construct validity using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in construct validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Criterion Validity; Content Validity; Predictive Biomarker Validity",
    "common_misinterpretations": "Treating construct validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000035",
    "api_endpoint_template": "/v1/metrics/BEMO:2000035/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000035_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 42,
    "source_record_hash": "5bd558ed006f260bde44545e9ab38951fc6c2e450b4d3cb07f929d1fcb479f4e",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 42; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000036",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000036",
    "preferred_label": "Content Validity",
    "normalized_label": "content_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which content supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses content validity using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in content validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Construct Validity; Predictive Biomarker Validity; Prognostic Biomarker Validity",
    "common_misinterpretations": "Treating content validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000036",
    "api_endpoint_template": "/v1/metrics/BEMO:2000036/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000036_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 43,
    "source_record_hash": "1ceb580fd3a672a7c14d44163bda2886dd03d14b99ce004f1db40aa485bb3e1b",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 43; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000037",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000037",
    "preferred_label": "Context-of-Use Validity",
    "normalized_label": "context_of_use_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which context-of-use supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses context-of-use validity using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in context-of-use validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Biomarker Clinical Relevance; Biomarker Qualification Strength; Biomarker Reliability",
    "common_misinterpretations": "Treating context-of-use validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000037",
    "api_endpoint_template": "/v1/metrics/BEMO:2000037/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000037_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 44,
    "source_record_hash": "170c4bee423f9901b11abd5c6c7203f1253da40dbd46a33c459bac07471058e8",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 44; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000038",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000038",
    "preferred_label": "Convergent Validity",
    "normalized_label": "convergent_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which convergent supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses convergent validity using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in convergent validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Known-Groups Validity; Discriminant Validity; Criterion Validity",
    "common_misinterpretations": "Treating convergent validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000038",
    "api_endpoint_template": "/v1/metrics/BEMO:2000038/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000038_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 45,
    "source_record_hash": "4ad4866845885f677cad74042f65b0303f2d26597ea694b76dfed4bc71fedd68",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 45; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000039",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000039",
    "preferred_label": "Criterion Validity",
    "normalized_label": "criterion_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which criterion supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses criterion validity using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in criterion validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Discriminant Validity; Construct Validity; Content Validity",
    "common_misinterpretations": "Treating criterion validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000039",
    "api_endpoint_template": "/v1/metrics/BEMO:2000039/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000039_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 46,
    "source_record_hash": "04af58cc2d88f851cf92e0d1960d29a74b3d8a5cf3525dda9579101a813732b2",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 46; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000040",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000040",
    "preferred_label": "Diagnostic Biomarker Validity",
    "normalized_label": "diagnostic_biomarker_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which diagnostic biomarker supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses diagnostic biomarker validity using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in diagnostic biomarker validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Prognostic Biomarker Validity; Pharmacodynamic Biomarker Validity; Monitoring Biomarker Validity",
    "common_misinterpretations": "Treating diagnostic biomarker validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000040",
    "api_endpoint_template": "/v1/metrics/BEMO:2000040/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000040_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 47,
    "source_record_hash": "b87f6768315d9d24a6505cd78867a8b0dc9310fbd10aa04b46856994c12562e5",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 47; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000041",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000041",
    "preferred_label": "Discriminant Validity",
    "normalized_label": "discriminant_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which discriminant supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses discriminant validity using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in discriminant validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Convergent Validity; Criterion Validity; Construct Validity",
    "common_misinterpretations": "Treating discriminant validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000041",
    "api_endpoint_template": "/v1/metrics/BEMO:2000041/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000041_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 48,
    "source_record_hash": "c0e22c7d45b8b17a4c9f1de5c7c7bb4e085d98eb667da8d43e452ea31955900b",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 48; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000042",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000042",
    "preferred_label": "Endpoint Reliability",
    "normalized_label": "endpoint_reliability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of endpoint reliability.",
    "what_it_measures": "Assesses endpoint reliability using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in endpoint reliability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Outcome Relevance; Endpoint Responsiveness; Minimal Clinically Important Difference Validity",
    "common_misinterpretations": "Treating endpoint reliability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000042",
    "api_endpoint_template": "/v1/metrics/BEMO:2000042/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000042_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 49,
    "source_record_hash": "e147bf4116de09d3c1bd6b5fb8081223589d31f54f697b6e869790830619757d",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 49; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000043",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000043",
    "preferred_label": "Endpoint Responsiveness",
    "normalized_label": "endpoint_responsiveness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of endpoint responsiveness.",
    "what_it_measures": "Assesses endpoint responsiveness using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in endpoint responsiveness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Endpoint Reliability; Minimal Clinically Important Difference Validity",
    "common_misinterpretations": "Treating endpoint responsiveness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000043",
    "api_endpoint_template": "/v1/metrics/BEMO:2000043/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000043_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 50,
    "source_record_hash": "3cb1f45a15a5daa5f6b98c2d745a57440f42e5840e757c82a744e9f010f76df0",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 50; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000044",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000044",
    "preferred_label": "Endpoint Validity",
    "normalized_label": "endpoint_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which endpoint supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses endpoint validity using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in endpoint validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Trial-Level Surrogacy; Outcome Relevance; Endpoint Reliability",
    "common_misinterpretations": "Treating endpoint validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000044",
    "api_endpoint_template": "/v1/metrics/BEMO:2000044/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000044_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 51,
    "source_record_hash": "f79c486fa1f56b17619593da318c44a3704cbd1294be41ae30a2b38ceb9410d1",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 51; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000045",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000045",
    "preferred_label": "Individual-Level Surrogacy",
    "normalized_label": "individual_level_surrogacy",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of individual-level surrogacy.",
    "what_it_measures": "Assesses individual-level surrogacy using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in individual-level surrogacy can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Surrogate Endpoint Validity; Trial-Level Surrogacy; Endpoint Validity",
    "common_misinterpretations": "Treating individual-level surrogacy as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000045",
    "api_endpoint_template": "/v1/metrics/BEMO:2000045/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000045_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 52,
    "source_record_hash": "4d46697f970727d741077ee1e1f9eeeaed4beee8d6ef96a339ca927181b91ef5",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 52; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000046",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000046",
    "preferred_label": "Known-Groups Validity",
    "normalized_label": "known_groups_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which known-groups supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses known-groups validity using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in known-groups validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Biomarker Sensitivity to Change; Convergent Validity; Discriminant Validity",
    "common_misinterpretations": "Treating known-groups validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000046",
    "api_endpoint_template": "/v1/metrics/BEMO:2000046/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000046_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 53,
    "source_record_hash": "8e195ef346deba393b7a3adaf4c77bfbd949dbf0f057cd9af26312568cb85421",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 53; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000047",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000047",
    "preferred_label": "Minimal Clinically Important Difference Validity",
    "normalized_label": "minimal_clinically_important_difference_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which minimal clinically important difference supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses minimal clinically important difference validity using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in minimal clinically important difference validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Endpoint Responsiveness",
    "common_misinterpretations": "Treating minimal clinically important difference validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000047",
    "api_endpoint_template": "/v1/metrics/BEMO:2000047/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000047_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 54,
    "source_record_hash": "604e83a95f413c6c8ddc8abe7ad03f24c441ede8e65d506baef0410866c23fa7",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 54; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000048",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000048",
    "preferred_label": "Monitoring Biomarker Validity",
    "normalized_label": "monitoring_biomarker_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which monitoring biomarker supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses monitoring biomarker validity using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in monitoring biomarker validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Pharmacodynamic Biomarker Validity; Safety Biomarker Validity; Susceptibility/Risk Biomarker Validity",
    "common_misinterpretations": "Treating monitoring biomarker validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000048",
    "api_endpoint_template": "/v1/metrics/BEMO:2000048/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000048_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 55,
    "source_record_hash": "cc605972d7119b4dabf5e0bc927d29fa05979e706703654bb3ea93c2ebe95461",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 55; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000049",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000049",
    "preferred_label": "Outcome Relevance",
    "normalized_label": "outcome_relevance",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of outcome relevance.",
    "what_it_measures": "Assesses outcome relevance using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in outcome relevance can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Endpoint Validity; Endpoint Reliability; Endpoint Responsiveness",
    "common_misinterpretations": "Treating outcome relevance as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000049",
    "api_endpoint_template": "/v1/metrics/BEMO:2000049/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000049_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 56,
    "source_record_hash": "1adca583ee04c245cdae3428bd050f3ed8796d29bf4b214b5880769da8977172",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 56; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000050",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000050",
    "preferred_label": "Pharmacodynamic Biomarker Validity",
    "normalized_label": "pharmacodynamic_biomarker_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which pharmacodynamic biomarker supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses pharmacodynamic biomarker validity using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in pharmacodynamic biomarker validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Diagnostic Biomarker Validity; Monitoring Biomarker Validity; Safety Biomarker Validity",
    "common_misinterpretations": "Treating pharmacodynamic biomarker validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000050",
    "api_endpoint_template": "/v1/metrics/BEMO:2000050/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000050_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 57,
    "source_record_hash": "4eb497c772907b7927e32ee929fba9a804b1c75888594041caa61dfab977440a",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 57; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000051",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000051",
    "preferred_label": "Predictive Biomarker Validity",
    "normalized_label": "predictive_biomarker_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which predictive biomarker supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses predictive biomarker validity using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in predictive biomarker validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Content Validity; Prognostic Biomarker Validity; Diagnostic Biomarker Validity",
    "common_misinterpretations": "Treating predictive biomarker validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000051",
    "api_endpoint_template": "/v1/metrics/BEMO:2000051/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000051_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 58,
    "source_record_hash": "c5c7cbb5b7738940f61731df207186f05f8ae71ecab7ca3c5588c823af8d00eb",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 58; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000052",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000052",
    "preferred_label": "Prognostic Biomarker Validity",
    "normalized_label": "prognostic_biomarker_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which prognostic biomarker supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses prognostic biomarker validity using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in prognostic biomarker validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Predictive Biomarker Validity; Diagnostic Biomarker Validity; Pharmacodynamic Biomarker Validity",
    "common_misinterpretations": "Treating prognostic biomarker validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000052",
    "api_endpoint_template": "/v1/metrics/BEMO:2000052/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000052_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 59,
    "source_record_hash": "2dd804ff14e01e089d83a5d2d6ef790d24cf90ca54d3426049116e4e7aeb095f",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 59; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000053",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000053",
    "preferred_label": "Response Biomarker Validity",
    "normalized_label": "response_biomarker_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which response biomarker supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses response biomarker validity using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in response biomarker validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Susceptibility/Risk Biomarker Validity; Surrogate Endpoint Validity; Individual-Level Surrogacy",
    "common_misinterpretations": "Treating response biomarker validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000053",
    "api_endpoint_template": "/v1/metrics/BEMO:2000053/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000053_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 60,
    "source_record_hash": "a8e8ef21a701fbb547c028557e4678bc79ebeda610eb6926bf0061b6e9a016c4",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 60; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000054",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000054",
    "preferred_label": "Safety Biomarker Validity",
    "normalized_label": "safety_biomarker_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which safety biomarker supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses safety biomarker validity using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in safety biomarker validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Monitoring Biomarker Validity; Susceptibility/Risk Biomarker Validity; Response Biomarker Validity",
    "common_misinterpretations": "Treating safety biomarker validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000054",
    "api_endpoint_template": "/v1/metrics/BEMO:2000054/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000054_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 61,
    "source_record_hash": "a6b6c6cf8ada87a1112583df9bc78595f4f0975ec0e8bbfc01ca6f00c2c0adf1",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 61; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000055",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000055",
    "preferred_label": "Surrogate Endpoint Validity",
    "normalized_label": "surrogate_endpoint_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which surrogate endpoint supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses surrogate endpoint validity using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in surrogate endpoint validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Response Biomarker Validity; Individual-Level Surrogacy; Trial-Level Surrogacy",
    "common_misinterpretations": "Treating surrogate endpoint validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000055",
    "api_endpoint_template": "/v1/metrics/BEMO:2000055/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000055_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 62,
    "source_record_hash": "880b1c4a9fa2a25e2876679a2a7e759365591c8d0d0ae431e9a6e89a9d327bd9",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 62; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000056",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000056",
    "preferred_label": "Susceptibility/Risk Biomarker Validity",
    "normalized_label": "susceptibility_risk_biomarker_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that susceptibility/risk biomarker validity introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses susceptibility/risk biomarker validity using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in susceptibility/risk biomarker validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Safety Biomarker Validity; Response Biomarker Validity; Surrogate Endpoint Validity",
    "common_misinterpretations": "Treating susceptibility/risk biomarker validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000056",
    "api_endpoint_template": "/v1/metrics/BEMO:2000056/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000056_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 63,
    "source_record_hash": "596927f557190db71a0b686158bde6134cafa9cdb9c1876784270d91a80452f5",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 63; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000057",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000057",
    "preferred_label": "Trial-Level Surrogacy",
    "normalized_label": "trial_level_surrogacy",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100002",
    "category_label": "Biomarker and Endpoint Validation",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100002",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of trial-level surrogacy.",
    "what_it_measures": "Assesses trial-level surrogacy using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in trial-level surrogacy can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "related_frameworks_source": "FDA Biomarker; BEST; EMA E16; REMARK",
    "closely_related_metrics_source": "Individual-Level Surrogacy; Endpoint Validity; Outcome Relevance",
    "common_misinterpretations": "Treating trial-level surrogacy as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Biomarker development, qualification, endpoint and surrogate validation studies",
    "domain_applicability": "Biomarker and Endpoint Validation",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000057",
    "api_endpoint_template": "/v1/metrics/BEMO:2000057/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000057_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 64,
    "source_record_hash": "977d5f2b7e02b5e90f442ea4e8788e2fe539316cddda3ae61da29b0fa71c5325",
    "source_references": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 64; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://www.ncbi.nlm.nih.gov/books/NBK326791/ | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000058",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000058",
    "preferred_label": "Anatomical Site Fidelity",
    "normalized_label": "anatomical_site_fidelity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100003",
    "category_label": "Biospecimen and Preanalytical Quality",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100003",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of anatomical site fidelity.",
    "what_it_measures": "Assesses anatomical site fidelity using evidence appropriate to biospecimen and preanalytical quality, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in anatomical site fidelity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "All studies using human or animal biospecimens",
    "related_frameworks_source": "BRISQ; ISO 15189; REMARK",
    "closely_related_metrics_source": "Processing Delay Control; Pathology Confirmation; Tumor Purity",
    "common_misinterpretations": "Treating anatomical site fidelity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "All studies using human or animal biospecimens",
    "domain_applicability": "Biospecimen and Preanalytical Quality",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000058",
    "api_endpoint_template": "/v1/metrics/BEMO:2000058/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000058_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 65,
    "source_record_hash": "8fa3b411fb892fff8cc31c078e25770eb74980a525cbc8e76d63bcb0f15bdaf8",
    "source_references": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 65; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000059",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000059",
    "preferred_label": "Biospecimen Integrity",
    "normalized_label": "biospecimen_integrity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100003",
    "category_label": "Biospecimen and Preanalytical Quality",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100003",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of biospecimen integrity.",
    "what_it_measures": "Assesses biospecimen integrity using evidence appropriate to biospecimen and preanalytical quality, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in biospecimen integrity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "All studies using human or animal biospecimens",
    "related_frameworks_source": "BRISQ; ISO 15189; REMARK",
    "closely_related_metrics_source": "Biospecimen Provenance Completeness; Collection Procedure Consistency",
    "common_misinterpretations": "Treating biospecimen integrity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "All studies using human or animal biospecimens",
    "domain_applicability": "Biospecimen and Preanalytical Quality",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000059",
    "api_endpoint_template": "/v1/metrics/BEMO:2000059/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000059_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 66,
    "source_record_hash": "b89a21b15f8ca110af0a2e2a28ae4ce7939819f7d62769c459c1cd5dc9b712cc",
    "source_references": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 66; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000060",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000060",
    "preferred_label": "Biospecimen Provenance Completeness",
    "normalized_label": "biospecimen_provenance_completeness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100003",
    "category_label": "Biospecimen and Preanalytical Quality",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100003",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which all scientifically necessary components of biospecimen provenance are present, documented, and evaluable.",
    "what_it_measures": "Assesses biospecimen provenance completeness using evidence appropriate to biospecimen and preanalytical quality, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in biospecimen provenance completeness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "All studies using human or animal biospecimens",
    "related_frameworks_source": "BRISQ; ISO 15189; REMARK",
    "closely_related_metrics_source": "Biospecimen Integrity; Collection Procedure Consistency; Warm Ischemia Control",
    "common_misinterpretations": "Treating biospecimen provenance completeness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "All studies using human or animal biospecimens",
    "domain_applicability": "Biospecimen and Preanalytical Quality",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000060",
    "api_endpoint_template": "/v1/metrics/BEMO:2000060/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000060_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 67,
    "source_record_hash": "c859051c1fe5f3cb60cda0bb4dcf804459be135ee18bb1bb44d89345dea50253",
    "source_references": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 67; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000061",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000061",
    "preferred_label": "Cellularity Adequacy",
    "normalized_label": "cellularity_adequacy",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100003",
    "category_label": "Biospecimen and Preanalytical Quality",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100003",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which cellularity is sufficient and fit for the stated biomedical inference.",
    "what_it_measures": "Assesses cellularity adequacy using evidence appropriate to biospecimen and preanalytical quality, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in cellularity adequacy can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "All studies using human or animal biospecimens",
    "related_frameworks_source": "BRISQ; ISO 15189; REMARK",
    "closely_related_metrics_source": "Tumor Purity; Necrosis Burden; Hemolysis Burden",
    "common_misinterpretations": "Treating cellularity adequacy as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "All studies using human or animal biospecimens",
    "domain_applicability": "Biospecimen and Preanalytical Quality",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000061",
    "api_endpoint_template": "/v1/metrics/BEMO:2000061/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000061_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 68,
    "source_record_hash": "de5efa73121b798bb0e1a53bddae9ef743d4a522e6df52007a5b7569bc63e020",
    "source_references": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 68; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000062",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000062",
    "preferred_label": "Chain-of-Custody Integrity",
    "normalized_label": "chain_of_custody_integrity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100003",
    "category_label": "Biospecimen and Preanalytical Quality",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100003",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of chain-of-custody integrity.",
    "what_it_measures": "Assesses chain-of-custody integrity using evidence appropriate to biospecimen and preanalytical quality, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in chain-of-custody integrity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "All studies using human or animal biospecimens",
    "related_frameworks_source": "BRISQ; ISO 15189; REMARK",
    "closely_related_metrics_source": "Microbial Contamination; Matched-Sample Integrity",
    "common_misinterpretations": "Treating chain-of-custody integrity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "All studies using human or animal biospecimens",
    "domain_applicability": "Biospecimen and Preanalytical Quality",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000062",
    "api_endpoint_template": "/v1/metrics/BEMO:2000062/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000062_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 69,
    "source_record_hash": "38ecb99023f4b12b1bfca7d66221917ae384546ef170c868cd32fb2eb70f3f40",
    "source_references": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 69; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000063",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000063",
    "preferred_label": "Cold Ischemia Control",
    "normalized_label": "cold_ischemia_control",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100003",
    "category_label": "Biospecimen and Preanalytical Quality",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100003",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of cold ischemia control.",
    "what_it_measures": "Assesses cold ischemia control using evidence appropriate to biospecimen and preanalytical quality, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in cold ischemia control can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "All studies using human or animal biospecimens",
    "related_frameworks_source": "BRISQ; ISO 15189; REMARK",
    "closely_related_metrics_source": "Warm Ischemia Control; Time-to-Fixation Adequacy; Fixation Adequacy",
    "common_misinterpretations": "Treating cold ischemia control as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "All studies using human or animal biospecimens",
    "domain_applicability": "Biospecimen and Preanalytical Quality",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000063",
    "api_endpoint_template": "/v1/metrics/BEMO:2000063/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000063_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 70,
    "source_record_hash": "450f9e94b009036abe7a13fe3055116e7c4959857a7291ed7e337a746d7bf722",
    "source_references": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 70; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000064",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000064",
    "preferred_label": "Collection Procedure Consistency",
    "normalized_label": "collection_procedure_consistency",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100003",
    "category_label": "Biospecimen and Preanalytical Quality",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100003",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree of agreement in collection procedure across measurements, studies, methods, populations, or biological levels.",
    "what_it_measures": "Assesses collection procedure consistency using evidence appropriate to biospecimen and preanalytical quality, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in collection procedure consistency can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "All studies using human or animal biospecimens",
    "related_frameworks_source": "BRISQ; ISO 15189; REMARK",
    "closely_related_metrics_source": "Biospecimen Provenance Completeness; Warm Ischemia Control; Cold Ischemia Control",
    "common_misinterpretations": "Treating collection procedure consistency as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "All studies using human or animal biospecimens",
    "domain_applicability": "Biospecimen and Preanalytical Quality",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000064",
    "api_endpoint_template": "/v1/metrics/BEMO:2000064/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000064_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 71,
    "source_record_hash": "c748a49d52923f74e8e31a0f69a4e91ee50970289d8b43c903a638e0573cc828",
    "source_references": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 71; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000065",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000065",
    "preferred_label": "DNA Integrity",
    "normalized_label": "dna_integrity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100003",
    "category_label": "Biospecimen and Preanalytical Quality",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100003",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of dna integrity.",
    "what_it_measures": "Assesses dna integrity using evidence appropriate to biospecimen and preanalytical quality, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in dna integrity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "All studies using human or animal biospecimens",
    "related_frameworks_source": "BRISQ; ISO 15189; REMARK",
    "closely_related_metrics_source": "RNA Integrity; Protein Integrity; Microbial Contamination",
    "common_misinterpretations": "Treating dna integrity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "All studies using human or animal biospecimens",
    "domain_applicability": "Biospecimen and Preanalytical Quality",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000065",
    "api_endpoint_template": "/v1/metrics/BEMO:2000065/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000065_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 72,
    "source_record_hash": "494036e6478a34bfe608bc3b1267e04a777d16e96430109ab2ba9b01e99c6693",
    "source_references": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 72; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000066",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000066",
    "preferred_label": "Fixation Adequacy",
    "normalized_label": "fixation_adequacy",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100003",
    "category_label": "Biospecimen and Preanalytical Quality",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100003",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which fixation is sufficient and fit for the stated biomedical inference.",
    "what_it_measures": "Assesses fixation adequacy using evidence appropriate to biospecimen and preanalytical quality, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in fixation adequacy can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "All studies using human or animal biospecimens",
    "related_frameworks_source": "BRISQ; ISO 15189; REMARK",
    "closely_related_metrics_source": "Time-to-Fixation Adequacy; Preservation Adequacy; Storage Temperature Control",
    "common_misinterpretations": "Treating fixation adequacy as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "All studies using human or animal biospecimens",
    "domain_applicability": "Biospecimen and Preanalytical Quality",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000066",
    "api_endpoint_template": "/v1/metrics/BEMO:2000066/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000066_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 73,
    "source_record_hash": "c08e61688a36fec680e9073fc8888dbfd98852919e3f7ccf7c3180ed49d1e921",
    "source_references": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 73; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000067",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000067",
    "preferred_label": "Freeze–Thaw Burden",
    "normalized_label": "freeze_thaw_burden",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100003",
    "category_label": "Biospecimen and Preanalytical Quality",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100003",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of freeze–thaw burden.",
    "what_it_measures": "Assesses freeze–thaw burden using evidence appropriate to biospecimen and preanalytical quality, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in freeze–thaw burden can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "All studies using human or animal biospecimens",
    "related_frameworks_source": "BRISQ; ISO 15189; REMARK",
    "closely_related_metrics_source": "Storage Temperature Control; Transport Condition Integrity; Processing Delay Control",
    "common_misinterpretations": "Treating freeze–thaw burden as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "All studies using human or animal biospecimens",
    "domain_applicability": "Biospecimen and Preanalytical Quality",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000067",
    "api_endpoint_template": "/v1/metrics/BEMO:2000067/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000067_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 74,
    "source_record_hash": "40c5c886eacc67a9addeaa92c47d69bf9fbd4b1d2a0042a2efd3611fd5cebb4b",
    "source_references": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 74; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000068",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000068",
    "preferred_label": "Hemolysis Burden",
    "normalized_label": "hemolysis_burden",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100003",
    "category_label": "Biospecimen and Preanalytical Quality",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100003",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of hemolysis burden.",
    "what_it_measures": "Assesses hemolysis burden using evidence appropriate to biospecimen and preanalytical quality, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in hemolysis burden can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "All studies using human or animal biospecimens",
    "related_frameworks_source": "BRISQ; ISO 15189; REMARK",
    "closely_related_metrics_source": "Necrosis Burden; Lipemia Burden; Icterus Interference",
    "common_misinterpretations": "Treating hemolysis burden as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "All studies using human or animal biospecimens",
    "domain_applicability": "Biospecimen and Preanalytical Quality",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000068",
    "api_endpoint_template": "/v1/metrics/BEMO:2000068/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000068_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 75,
    "source_record_hash": "1b0946c6b109834d9e6fa6dc5ae7dde1ce95bc65f999a58a3c5a88bc66c6a47c",
    "source_references": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 75; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000069",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000069",
    "preferred_label": "Icterus Interference",
    "normalized_label": "icterus_interference",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100003",
    "category_label": "Biospecimen and Preanalytical Quality",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100003",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of icterus interference.",
    "what_it_measures": "Assesses icterus interference using evidence appropriate to biospecimen and preanalytical quality, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in icterus interference can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Replicate dilution series; blank and spiked samples; reference materials; method-comparison studies; predefined CLSI/ISO acceptance criteria.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "All studies using human or animal biospecimens",
    "related_frameworks_source": "BRISQ; ISO 15189; REMARK",
    "closely_related_metrics_source": "Lipemia Burden; RNA Integrity; DNA Integrity",
    "common_misinterpretations": "Treating icterus interference as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "All studies using human or animal biospecimens",
    "domain_applicability": "Biospecimen and Preanalytical Quality",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000069",
    "api_endpoint_template": "/v1/metrics/BEMO:2000069/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000069_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 76,
    "source_record_hash": "d0f3346c9caa8abb9b49bded0ab6e26e5f13d5a8fb5a20971f64067dd82054ea",
    "source_references": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 76; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000070",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000070",
    "preferred_label": "Lipemia Burden",
    "normalized_label": "lipemia_burden",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100003",
    "category_label": "Biospecimen and Preanalytical Quality",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100003",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of lipemia burden.",
    "what_it_measures": "Assesses lipemia burden using evidence appropriate to biospecimen and preanalytical quality, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in lipemia burden can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "All studies using human or animal biospecimens",
    "related_frameworks_source": "BRISQ; ISO 15189; REMARK",
    "closely_related_metrics_source": "Hemolysis Burden; Icterus Interference; RNA Integrity",
    "common_misinterpretations": "Treating lipemia burden as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "All studies using human or animal biospecimens",
    "domain_applicability": "Biospecimen and Preanalytical Quality",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000070",
    "api_endpoint_template": "/v1/metrics/BEMO:2000070/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000070_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 77,
    "source_record_hash": "572ca1cf50802a5447be4c1286cdad2930a7ec08e97e7b9af663a3cb66e1d788",
    "source_references": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 77; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000071",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000071",
    "preferred_label": "Matched-Sample Integrity",
    "normalized_label": "matched_sample_integrity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100003",
    "category_label": "Biospecimen and Preanalytical Quality",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100003",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of matched-sample integrity.",
    "what_it_measures": "Assesses matched-sample integrity using evidence appropriate to biospecimen and preanalytical quality, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in matched-sample integrity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "All studies using human or animal biospecimens",
    "related_frameworks_source": "BRISQ; ISO 15189; REMARK",
    "closely_related_metrics_source": "Chain-of-Custody Integrity",
    "common_misinterpretations": "Treating matched-sample integrity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "All studies using human or animal biospecimens",
    "domain_applicability": "Biospecimen and Preanalytical Quality",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000071",
    "api_endpoint_template": "/v1/metrics/BEMO:2000071/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000071_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 78,
    "source_record_hash": "daf35eaf7e6632e499a494b9ba629171cde4aa96d4d637ad7669da2f69668fd5",
    "source_references": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 78; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000072",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000072",
    "preferred_label": "Microbial Contamination",
    "normalized_label": "microbial_contamination",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100003",
    "category_label": "Biospecimen and Preanalytical Quality",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100003",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of microbial contamination.",
    "what_it_measures": "Assesses microbial contamination using evidence appropriate to biospecimen and preanalytical quality, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in microbial contamination can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "All studies using human or animal biospecimens",
    "related_frameworks_source": "BRISQ; ISO 15189; REMARK",
    "closely_related_metrics_source": "Protein Integrity; Chain-of-Custody Integrity; Matched-Sample Integrity",
    "common_misinterpretations": "Treating microbial contamination as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "All studies using human or animal biospecimens",
    "domain_applicability": "Biospecimen and Preanalytical Quality",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000072",
    "api_endpoint_template": "/v1/metrics/BEMO:2000072/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000072_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 79,
    "source_record_hash": "a7e7bf9a47cefd808a5ba122413c735b8b095ffc84592451f9857f4fe080e389",
    "source_references": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 79; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000073",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000073",
    "preferred_label": "Necrosis Burden",
    "normalized_label": "necrosis_burden",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100003",
    "category_label": "Biospecimen and Preanalytical Quality",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100003",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of necrosis burden.",
    "what_it_measures": "Assesses necrosis burden using evidence appropriate to biospecimen and preanalytical quality, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in necrosis burden can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "All studies using human or animal biospecimens",
    "related_frameworks_source": "BRISQ; ISO 15189; REMARK",
    "closely_related_metrics_source": "Cellularity Adequacy; Hemolysis Burden; Lipemia Burden",
    "common_misinterpretations": "Treating necrosis burden as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "All studies using human or animal biospecimens",
    "domain_applicability": "Biospecimen and Preanalytical Quality",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000073",
    "api_endpoint_template": "/v1/metrics/BEMO:2000073/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000073_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 80,
    "source_record_hash": "33466881e023e8dc75d5f189be9da266f95f3bf8283fa46f9f4cff10e5af6f95",
    "source_references": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 80; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000074",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000074",
    "preferred_label": "Pathology Confirmation",
    "normalized_label": "pathology_confirmation",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100003",
    "category_label": "Biospecimen and Preanalytical Quality",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100003",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of pathology confirmation.",
    "what_it_measures": "Assesses pathology confirmation using evidence appropriate to biospecimen and preanalytical quality, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in pathology confirmation can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "All studies using human or animal biospecimens",
    "related_frameworks_source": "BRISQ; ISO 15189; REMARK",
    "closely_related_metrics_source": "Anatomical Site Fidelity; Tumor Purity; Cellularity Adequacy",
    "common_misinterpretations": "Treating pathology confirmation as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "All studies using human or animal biospecimens",
    "domain_applicability": "Biospecimen and Preanalytical Quality",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000074",
    "api_endpoint_template": "/v1/metrics/BEMO:2000074/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000074_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 81,
    "source_record_hash": "e470a75855d7bb24a7f3957922ccdf78961ef4c923b6f754c0006ebb46c0367e",
    "source_references": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 81; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000075",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000075",
    "preferred_label": "Preservation Adequacy",
    "normalized_label": "preservation_adequacy",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100003",
    "category_label": "Biospecimen and Preanalytical Quality",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100003",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which preservation is sufficient and fit for the stated biomedical inference.",
    "what_it_measures": "Assesses preservation adequacy using evidence appropriate to biospecimen and preanalytical quality, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in preservation adequacy can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "All studies using human or animal biospecimens",
    "related_frameworks_source": "BRISQ; ISO 15189; REMARK",
    "closely_related_metrics_source": "Fixation Adequacy; Storage Temperature Control; Freeze–Thaw Burden",
    "common_misinterpretations": "Treating preservation adequacy as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "All studies using human or animal biospecimens",
    "domain_applicability": "Biospecimen and Preanalytical Quality",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000075",
    "api_endpoint_template": "/v1/metrics/BEMO:2000075/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000075_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 82,
    "source_record_hash": "de3923232eba7ea0cab4f8eddc6a1539eac9f06416d7c31e6d2ce8fbf8492ba5",
    "source_references": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 82; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000076",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000076",
    "preferred_label": "Processing Delay Control",
    "normalized_label": "processing_delay_control",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100003",
    "category_label": "Biospecimen and Preanalytical Quality",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100003",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of processing delay control.",
    "what_it_measures": "Assesses processing delay control using evidence appropriate to biospecimen and preanalytical quality, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in processing delay control can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "All studies using human or animal biospecimens",
    "related_frameworks_source": "BRISQ; ISO 15189; REMARK",
    "closely_related_metrics_source": "Transport Condition Integrity; Anatomical Site Fidelity; Pathology Confirmation",
    "common_misinterpretations": "Treating processing delay control as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "All studies using human or animal biospecimens",
    "domain_applicability": "Biospecimen and Preanalytical Quality",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000076",
    "api_endpoint_template": "/v1/metrics/BEMO:2000076/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000076_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 83,
    "source_record_hash": "575df935e8ca0edd1975c05772eaa99f38b63f196b0ee598cef40ebcb4554aaf",
    "source_references": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 83; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000077",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000077",
    "preferred_label": "Protein Integrity",
    "normalized_label": "protein_integrity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100003",
    "category_label": "Biospecimen and Preanalytical Quality",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100003",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of protein integrity.",
    "what_it_measures": "Assesses protein integrity using evidence appropriate to biospecimen and preanalytical quality, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in protein integrity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Target-decoy analysis; spectral scoring; reference standards; replicate injections; retention-time and mass-error monitoring; orthogonal confirmation.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "All studies using human or animal biospecimens",
    "related_frameworks_source": "BRISQ; ISO 15189; REMARK",
    "closely_related_metrics_source": "DNA Integrity; Microbial Contamination; Chain-of-Custody Integrity",
    "common_misinterpretations": "Treating protein integrity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "All studies using human or animal biospecimens",
    "domain_applicability": "Biospecimen and Preanalytical Quality",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000077",
    "api_endpoint_template": "/v1/metrics/BEMO:2000077/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000077_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 84,
    "source_record_hash": "f776649240f851879898d488bb90516491936e0936f6f03ac5946be6c8b62a20",
    "source_references": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 84; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000078",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000078",
    "preferred_label": "RNA Integrity",
    "normalized_label": "rna_integrity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100003",
    "category_label": "Biospecimen and Preanalytical Quality",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100003",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of rna integrity.",
    "what_it_measures": "Assesses rna integrity using evidence appropriate to biospecimen and preanalytical quality, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in rna integrity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "All studies using human or animal biospecimens",
    "related_frameworks_source": "BRISQ; ISO 15189; REMARK",
    "closely_related_metrics_source": "Icterus Interference; DNA Integrity; Protein Integrity",
    "common_misinterpretations": "Treating rna integrity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "All studies using human or animal biospecimens",
    "domain_applicability": "Biospecimen and Preanalytical Quality",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000078",
    "api_endpoint_template": "/v1/metrics/BEMO:2000078/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000078_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 85,
    "source_record_hash": "98ac509f170b3163d862e8e08cc16dad8b915df5508f4e7394a8627d881f7350",
    "source_references": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 85; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000079",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000079",
    "preferred_label": "Storage Temperature Control",
    "normalized_label": "storage_temperature_control",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100003",
    "category_label": "Biospecimen and Preanalytical Quality",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100003",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of storage temperature control.",
    "what_it_measures": "Assesses storage temperature control using evidence appropriate to biospecimen and preanalytical quality, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in storage temperature control can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "All studies using human or animal biospecimens",
    "related_frameworks_source": "BRISQ; ISO 15189; REMARK",
    "closely_related_metrics_source": "Preservation Adequacy; Freeze–Thaw Burden; Transport Condition Integrity",
    "common_misinterpretations": "Treating storage temperature control as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "All studies using human or animal biospecimens",
    "domain_applicability": "Biospecimen and Preanalytical Quality",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000079",
    "api_endpoint_template": "/v1/metrics/BEMO:2000079/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000079_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 86,
    "source_record_hash": "b39a92acfa55bd840331823c88476d9d65ca0179f68f0f37ed8d7677a63d2193",
    "source_references": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 86; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000080",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000080",
    "preferred_label": "Time-to-Fixation Adequacy",
    "normalized_label": "time_to_fixation_adequacy",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100003",
    "category_label": "Biospecimen and Preanalytical Quality",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100003",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which time-to-fixation is sufficient and fit for the stated biomedical inference.",
    "what_it_measures": "Assesses time-to-fixation adequacy using evidence appropriate to biospecimen and preanalytical quality, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in time-to-fixation adequacy can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "All studies using human or animal biospecimens",
    "related_frameworks_source": "BRISQ; ISO 15189; REMARK",
    "closely_related_metrics_source": "Cold Ischemia Control; Fixation Adequacy; Preservation Adequacy",
    "common_misinterpretations": "Treating time-to-fixation adequacy as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "All studies using human or animal biospecimens",
    "domain_applicability": "Biospecimen and Preanalytical Quality",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000080",
    "api_endpoint_template": "/v1/metrics/BEMO:2000080/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000080_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 87,
    "source_record_hash": "49559a7ae628351af963a27a55893cf501098be34876ce35bdc2d4969fd4f94b",
    "source_references": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 87; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000081",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000081",
    "preferred_label": "Transport Condition Integrity",
    "normalized_label": "transport_condition_integrity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100003",
    "category_label": "Biospecimen and Preanalytical Quality",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100003",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of transport condition integrity.",
    "what_it_measures": "Assesses transport condition integrity using evidence appropriate to biospecimen and preanalytical quality, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in transport condition integrity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "All studies using human or animal biospecimens",
    "related_frameworks_source": "BRISQ; ISO 15189; REMARK",
    "closely_related_metrics_source": "Freeze–Thaw Burden; Processing Delay Control; Anatomical Site Fidelity",
    "common_misinterpretations": "Treating transport condition integrity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "All studies using human or animal biospecimens",
    "domain_applicability": "Biospecimen and Preanalytical Quality",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000081",
    "api_endpoint_template": "/v1/metrics/BEMO:2000081/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000081_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 88,
    "source_record_hash": "81f1c97831f3ffbcc8b4e89c16604f987d3fa2baac750496d710981c68a60598",
    "source_references": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 88; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000082",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000082",
    "preferred_label": "Tumor Purity",
    "normalized_label": "tumor_purity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100003",
    "category_label": "Biospecimen and Preanalytical Quality",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100003",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of tumor purity.",
    "what_it_measures": "Assesses tumor purity using evidence appropriate to biospecimen and preanalytical quality, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in tumor purity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "All studies using human or animal biospecimens",
    "related_frameworks_source": "BRISQ; ISO 15189; REMARK",
    "closely_related_metrics_source": "Pathology Confirmation; Cellularity Adequacy; Necrosis Burden",
    "common_misinterpretations": "Treating tumor purity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "All studies using human or animal biospecimens",
    "domain_applicability": "Biospecimen and Preanalytical Quality",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000082",
    "api_endpoint_template": "/v1/metrics/BEMO:2000082/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000082_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 89,
    "source_record_hash": "e7836bb1f6728d199c8634dbdbf560dae6243a3932920cc82164935a37c9180e",
    "source_references": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 89; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000083",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000083",
    "preferred_label": "Warm Ischemia Control",
    "normalized_label": "warm_ischemia_control",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100003",
    "category_label": "Biospecimen and Preanalytical Quality",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100003",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of warm ischemia control.",
    "what_it_measures": "Assesses warm ischemia control using evidence appropriate to biospecimen and preanalytical quality, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in warm ischemia control can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "All studies using human or animal biospecimens",
    "related_frameworks_source": "BRISQ; ISO 15189; REMARK",
    "closely_related_metrics_source": "Collection Procedure Consistency; Cold Ischemia Control; Time-to-Fixation Adequacy",
    "common_misinterpretations": "Treating warm ischemia control as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "All studies using human or animal biospecimens",
    "domain_applicability": "Biospecimen and Preanalytical Quality",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000083",
    "api_endpoint_template": "/v1/metrics/BEMO:2000083/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000083_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 90,
    "source_record_hash": "293c5ebda3d3695852f06644549a5b920266b83358bf49b383b5d90078fcdde6",
    "source_references": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 90; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/reporting-guidelines/brisq/ | https://www.iso.org/standard/76677.html | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000084",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000084",
    "preferred_label": "Assumption Sensitivity",
    "normalized_label": "assumption_sensitivity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100004",
    "category_label": "Causal Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100004",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of assumption sensitivity.",
    "what_it_measures": "Assesses assumption sensitivity using evidence appropriate to causal inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in assumption sensitivity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified threshold; valid reference standard; complete 2×2 classification; confidence intervals; spectrum and prevalence assessment.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "related_frameworks_source": "ROBINS-I; ROBINS-E; GRADE; STROBE; ICH E9",
    "closely_related_metrics_source": "E-value Strength; Falsification Test Support",
    "common_misinterpretations": "Treating assumption sensitivity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "domain_applicability": "Causal Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000084",
    "api_endpoint_template": "/v1/metrics/BEMO:2000084/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000084_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 91,
    "source_record_hash": "b75d62759fbd8f126f27997543f0f46dde1cb8c2484d156a08c9925c9476aa63",
    "source_references": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 91; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000085",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000085",
    "preferred_label": "Causal Contrast Clarity",
    "normalized_label": "causal_contrast_clarity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100004",
    "category_label": "Causal Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100004",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of causal contrast clarity.",
    "what_it_measures": "Assesses causal contrast clarity using evidence appropriate to causal inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in causal contrast clarity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Directed acyclic graphs; design emulation; balance diagnostics; negative controls; quantitative bias analysis; sensitivity and falsification analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "related_frameworks_source": "ROBINS-I; ROBINS-E; GRADE; STROBE; ICH E9",
    "closely_related_metrics_source": "Correct Temporal Ordering; Target Trial Emulation Fidelity; Instrument Validity",
    "common_misinterpretations": "Treating causal contrast clarity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "domain_applicability": "Causal Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000085",
    "api_endpoint_template": "/v1/metrics/BEMO:2000085/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000085_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 92,
    "source_record_hash": "d81e7f98cb339c656ef93d3243144295a2c872dc2bcb50f64863414984f27993",
    "source_references": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 92; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000086",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000086",
    "preferred_label": "Causal Identifiability",
    "normalized_label": "causal_identifiability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100004",
    "category_label": "Causal Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100004",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of causal identifiability.",
    "what_it_measures": "Assesses causal identifiability using evidence appropriate to causal inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in causal identifiability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Directed acyclic graphs; design emulation; balance diagnostics; negative controls; quantitative bias analysis; sensitivity and falsification analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "related_frameworks_source": "ROBINS-I; ROBINS-E; GRADE; STROBE; ICH E9",
    "closely_related_metrics_source": "Confounding Risk; Residual Confounding Risk",
    "common_misinterpretations": "Treating causal identifiability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "domain_applicability": "Causal Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000086",
    "api_endpoint_template": "/v1/metrics/BEMO:2000086/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000086_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 93,
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    "source_references": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 93; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000087",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000087",
    "preferred_label": "Collider Bias Risk",
    "normalized_label": "collider_bias_risk",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100004",
    "category_label": "Causal Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100004",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that collider bias introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses collider bias risk using evidence appropriate to causal inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in collider bias risk can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "related_frameworks_source": "ROBINS-I; ROBINS-E; GRADE; STROBE; ICH E9",
    "closely_related_metrics_source": "Effect-Modification Credibility; Time-Varying Confounding Control; Immortal-Time Bias Risk",
    "common_misinterpretations": "Treating collider bias risk as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "domain_applicability": "Causal Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000087",
    "api_endpoint_template": "/v1/metrics/BEMO:2000087/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000087_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 94,
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    "source_references": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 94; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000088",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000088",
    "preferred_label": "Confounding Risk",
    "normalized_label": "confounding_risk",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100004",
    "category_label": "Causal Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100004",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that confounding introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses confounding risk using evidence appropriate to causal inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in confounding risk can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Directed acyclic graphs; design emulation; balance diagnostics; negative controls; quantitative bias analysis; sensitivity and falsification analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "related_frameworks_source": "ROBINS-I; ROBINS-E; GRADE; STROBE; ICH E9",
    "closely_related_metrics_source": "Causal Identifiability; Residual Confounding Risk; Unmeasured Confounding Sensitivity",
    "common_misinterpretations": "Treating confounding risk as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "domain_applicability": "Causal Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000088",
    "api_endpoint_template": "/v1/metrics/BEMO:2000088/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000088_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 95,
    "source_record_hash": "cebd58c93ed86b363870e131c5d23217522d15af0abb7eac8956ec81e8515565",
    "source_references": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 95; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000089",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000089",
    "preferred_label": "Consistency Assumption Plausibility",
    "normalized_label": "consistency_assumption_plausibility",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100004",
    "category_label": "Causal Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100004",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree of agreement in consistency assumption plausibility across measurements, studies, methods, populations, or biological levels.",
    "what_it_measures": "Assesses consistency assumption plausibility using evidence appropriate to causal inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in consistency assumption plausibility can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "related_frameworks_source": "ROBINS-I; ROBINS-E; GRADE; STROBE; ICH E9",
    "closely_related_metrics_source": "Positivity Adequacy; No-Interference Plausibility; Correct Temporal Ordering",
    "common_misinterpretations": "Treating consistency assumption plausibility as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "domain_applicability": "Causal Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000089",
    "api_endpoint_template": "/v1/metrics/BEMO:2000089/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000089_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 96,
    "source_record_hash": "1bec3d5308662b9b5fad28978574efe7573d32766cf45ac34286863d2d2267a8",
    "source_references": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 96; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000090",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000090",
    "preferred_label": "Correct Temporal Ordering",
    "normalized_label": "correct_temporal_ordering",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100004",
    "category_label": "Causal Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100004",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of correct temporal ordering.",
    "what_it_measures": "Assesses correct temporal ordering using evidence appropriate to causal inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in correct temporal ordering can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "related_frameworks_source": "ROBINS-I; ROBINS-E; GRADE; STROBE; ICH E9",
    "closely_related_metrics_source": "No-Interference Plausibility; Causal Contrast Clarity; Target Trial Emulation Fidelity",
    "common_misinterpretations": "Treating correct temporal ordering as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "domain_applicability": "Causal Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000090",
    "api_endpoint_template": "/v1/metrics/BEMO:2000090/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000090_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 97,
    "source_record_hash": "b11d505f3985b03d1ab78fe50a79558d187aeacc3fabbc39b5dc3da61a0cfbe2",
    "source_references": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 97; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000091",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000091",
    "preferred_label": "Dechallenge–Rechallenge Support",
    "normalized_label": "dechallenge_rechallenge_support",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100004",
    "category_label": "Causal Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100004",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting dechallenge–rechallenge.",
    "what_it_measures": "Assesses dechallenge–rechallenge support using evidence appropriate to causal inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in dechallenge–rechallenge support can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "related_frameworks_source": "ROBINS-I; ROBINS-E; GRADE; STROBE; ICH E9",
    "closely_related_metrics_source": "Dose–Response Support; Mediation Evidence Strength; Effect-Modification Credibility",
    "common_misinterpretations": "Treating dechallenge–rechallenge support as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "domain_applicability": "Causal Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000091",
    "api_endpoint_template": "/v1/metrics/BEMO:2000091/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000091_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 98,
    "source_record_hash": "9e166f37b12b35c895b18fc7e56e04526e22004c0b70dee562c1cf80c5d17e69",
    "source_references": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 98; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000092",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000092",
    "preferred_label": "Dose–Response Support",
    "normalized_label": "dose_response_support",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100004",
    "category_label": "Causal Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100004",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting dose–response.",
    "what_it_measures": "Assesses dose–response support using evidence appropriate to causal inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in dose–response support can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Method- and analyte-specific physical units",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "related_frameworks_source": "ROBINS-I; ROBINS-E; GRADE; STROBE; ICH E9",
    "closely_related_metrics_source": "Negative-Control Validation; Dechallenge–Rechallenge Support; Mediation Evidence Strength",
    "common_misinterpretations": "Treating dose–response support as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "PhysicalMeasurementScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Method- and analyte-specific physical units",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ValidatedMeasurementProcedure",
    "computation_readiness": "DomainProtocolRequired",
    "formula_status": "MethodSpecificProtocolRequired",
    "human_readable_formula": "Apply a validated analyte- and method-specific measurement procedure with calibration and quality control.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"unitRef\":\"REQUIRED\"}",
    "required_inputs": "specimen_or_material; measurement_procedure; calibration_reference; quality_control_results; unit",
    "optional_inputs": "replicate_measurements; environmental_conditions; instrument_version",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "domain_applicability": "Causal Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "validated assay measurement",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000092",
    "api_endpoint_template": "/v1/metrics/BEMO:2000092/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000092_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 99,
    "source_record_hash": "75f662d9e2ee059c317733c8704b2f0f1f234146f1b2920ed572ec892b5a2d41",
    "source_references": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 99; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000093",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000093",
    "preferred_label": "E-value Strength",
    "normalized_label": "e_value_strength",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100004",
    "category_label": "Causal Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100004",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting e-value.",
    "what_it_measures": "Assesses e-value strength using evidence appropriate to causal inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in e-value strength can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ratio scale; null typically 1",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "related_frameworks_source": "ROBINS-I; ROBINS-E; GRADE; STROBE; ICH E9",
    "closely_related_metrics_source": "Quantitative Bias Analysis Robustness; Assumption Sensitivity; Falsification Test Support",
    "common_misinterpretations": "Treating e-value strength as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Specialized / infrequent",
    "maturity_of_metric": "Developing",
    "references_source": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RatioScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ratio scale; null typically 1",
    "minimum_value": 0.0,
    "maximum_value": null,
    "null_value": 1.0,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeRatioComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator; the null value is typically 1 where scientifically applicable",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator != 0\"],\"null_value\":1}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "confidence_level; stratum",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Not generally required unless converted to a probability or score.",
    "validation_status": "Source maturity: Developing; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "domain_applicability": "Causal Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "ratio estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000093",
    "api_endpoint_template": "/v1/metrics/BEMO:2000093/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000093_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 100,
    "source_record_hash": "8587ae49790e995db7d3bf84506f3bebdce4263532f6e5dcbd136229f5da442f",
    "source_references": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 100; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000094",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000094",
    "preferred_label": "Effect-Modification Credibility",
    "normalized_label": "effect_modification_credibility",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100004",
    "category_label": "Causal Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100004",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of effect-modification credibility.",
    "what_it_measures": "Assesses effect-modification credibility using evidence appropriate to causal inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in effect-modification credibility can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "related_frameworks_source": "ROBINS-I; ROBINS-E; GRADE; STROBE; ICH E9",
    "closely_related_metrics_source": "Mediation Evidence Strength; Collider Bias Risk; Time-Varying Confounding Control",
    "common_misinterpretations": "Treating effect-modification credibility as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "domain_applicability": "Causal Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000094",
    "api_endpoint_template": "/v1/metrics/BEMO:2000094/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000094_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 101,
    "source_record_hash": "f66521085db07e7bd17f7b93b07cf74e57b1c85461a2555c1146f672069098b2",
    "source_references": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 101; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000095",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000095",
    "preferred_label": "Exchangeability Plausibility",
    "normalized_label": "exchangeability_plausibility",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100004",
    "category_label": "Causal Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100004",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of exchangeability plausibility.",
    "what_it_measures": "Assesses exchangeability plausibility using evidence appropriate to causal inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in exchangeability plausibility can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Directed acyclic graphs; design emulation; balance diagnostics; negative controls; quantitative bias analysis; sensitivity and falsification analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "related_frameworks_source": "ROBINS-I; ROBINS-E; GRADE; STROBE; ICH E9",
    "closely_related_metrics_source": "Unmeasured Confounding Sensitivity; Positivity Adequacy; Consistency Assumption Plausibility",
    "common_misinterpretations": "Treating exchangeability plausibility as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "domain_applicability": "Causal Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000095",
    "api_endpoint_template": "/v1/metrics/BEMO:2000095/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000095_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 102,
    "source_record_hash": "7f4004986e0cd5fd0b8462346aec167d3be6e60fe67bb8a5838de7a005fd58d1",
    "source_references": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 102; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000096",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000096",
    "preferred_label": "Falsification Test Support",
    "normalized_label": "falsification_test_support",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100004",
    "category_label": "Causal Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100004",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting falsification test.",
    "what_it_measures": "Assesses falsification test support using evidence appropriate to causal inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in falsification test support can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "related_frameworks_source": "ROBINS-I; ROBINS-E; GRADE; STROBE; ICH E9",
    "closely_related_metrics_source": "Assumption Sensitivity",
    "common_misinterpretations": "Treating falsification test support as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "domain_applicability": "Causal Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000096",
    "api_endpoint_template": "/v1/metrics/BEMO:2000096/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000096_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 103,
    "source_record_hash": "280760fd65dbda26ef711b182bed36c1b7e3679af41be52e50dfca26f92b3400",
    "source_references": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 103; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000097",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000097",
    "preferred_label": "Immortal-Time Bias Risk",
    "normalized_label": "immortal_time_bias_risk",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100004",
    "category_label": "Causal Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100004",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that immortal-time bias introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses immortal-time bias risk using evidence appropriate to causal inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in immortal-time bias risk can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "related_frameworks_source": "ROBINS-I; ROBINS-E; GRADE; STROBE; ICH E9",
    "closely_related_metrics_source": "Time-Varying Confounding Control; Reverse-Causation Risk; Selection-on-Survival Bias Risk",
    "common_misinterpretations": "Treating immortal-time bias risk as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "domain_applicability": "Causal Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000097",
    "api_endpoint_template": "/v1/metrics/BEMO:2000097/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000097_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 104,
    "source_record_hash": "21a510319cb99a940f9fc99111522f80932b8a874f1ea984fb332f8f218483c8",
    "source_references": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 104; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000098",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000098",
    "preferred_label": "Instrument Validity",
    "normalized_label": "instrument_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100004",
    "category_label": "Causal Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100004",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which instrument supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses instrument validity using evidence appropriate to causal inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in instrument validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "related_frameworks_source": "ROBINS-I; ROBINS-E; GRADE; STROBE; ICH E9",
    "closely_related_metrics_source": "Target Trial Emulation Fidelity; Negative-Control Validation; Dose–Response Support",
    "common_misinterpretations": "Treating instrument validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "domain_applicability": "Causal Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000098",
    "api_endpoint_template": "/v1/metrics/BEMO:2000098/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000098_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 105,
    "source_record_hash": "e7033f91a59f115f9fba748b04cab66664ac151f4c8d653ea61aa823a8c6cce4",
    "source_references": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 105; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000099",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000099",
    "preferred_label": "Mediation Evidence Strength",
    "normalized_label": "mediation_evidence_strength",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100004",
    "category_label": "Causal Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100004",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting mediation evidence.",
    "what_it_measures": "Assesses mediation evidence strength using evidence appropriate to causal inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in mediation evidence strength can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "related_frameworks_source": "ROBINS-I; ROBINS-E; GRADE; STROBE; ICH E9",
    "closely_related_metrics_source": "Dechallenge–Rechallenge Support; Effect-Modification Credibility; Collider Bias Risk",
    "common_misinterpretations": "Treating mediation evidence strength as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "domain_applicability": "Causal Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000099",
    "api_endpoint_template": "/v1/metrics/BEMO:2000099/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000099_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 106,
    "source_record_hash": "b7abd5f34cd2addb34f26d923a9c80b402d8914f57510a7f5fe8c4ed41659c58",
    "source_references": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 106; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000100",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000100",
    "preferred_label": "Negative-Control Validation",
    "normalized_label": "negative_control_validation",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100004",
    "category_label": "Causal Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100004",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of negative-control validation.",
    "what_it_measures": "Assesses negative-control validation using evidence appropriate to causal inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in negative-control validation can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "related_frameworks_source": "ROBINS-I; ROBINS-E; GRADE; STROBE; ICH E9",
    "closely_related_metrics_source": "Instrument Validity; Dose–Response Support; Dechallenge–Rechallenge Support",
    "common_misinterpretations": "Treating negative-control validation as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "domain_applicability": "Causal Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000100",
    "api_endpoint_template": "/v1/metrics/BEMO:2000100/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000100_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 107,
    "source_record_hash": "63bedc3fc09ef48160a8d522d76618e50e47197d3d502ae109f1015d0fbcb67e",
    "source_references": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 107; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000101",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000101",
    "preferred_label": "No-Interference Plausibility",
    "normalized_label": "no_interference_plausibility",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100004",
    "category_label": "Causal Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100004",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of no-interference plausibility.",
    "what_it_measures": "Assesses no-interference plausibility using evidence appropriate to causal inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in no-interference plausibility can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Replicate dilution series; blank and spiked samples; reference materials; method-comparison studies; predefined CLSI/ISO acceptance criteria.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "related_frameworks_source": "ROBINS-I; ROBINS-E; GRADE; STROBE; ICH E9",
    "closely_related_metrics_source": "Consistency Assumption Plausibility; Correct Temporal Ordering; Causal Contrast Clarity",
    "common_misinterpretations": "Treating no-interference plausibility as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "domain_applicability": "Causal Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000101",
    "api_endpoint_template": "/v1/metrics/BEMO:2000101/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000101_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 108,
    "source_record_hash": "8aa9a1ba76fa5fd8217fff1b4352656d262602a1040dc8618b138b2e37a93d9a",
    "source_references": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 108; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000102",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000102",
    "preferred_label": "Positivity Adequacy",
    "normalized_label": "positivity_adequacy",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100004",
    "category_label": "Causal Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100004",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which positivity is sufficient and fit for the stated biomedical inference.",
    "what_it_measures": "Assesses positivity adequacy using evidence appropriate to causal inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in positivity adequacy can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Directed acyclic graphs; design emulation; balance diagnostics; negative controls; quantitative bias analysis; sensitivity and falsification analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "related_frameworks_source": "ROBINS-I; ROBINS-E; GRADE; STROBE; ICH E9",
    "closely_related_metrics_source": "Exchangeability Plausibility; Consistency Assumption Plausibility; No-Interference Plausibility",
    "common_misinterpretations": "Treating positivity adequacy as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "domain_applicability": "Causal Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000102",
    "api_endpoint_template": "/v1/metrics/BEMO:2000102/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000102_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 109,
    "source_record_hash": "be2ac5c0345d954f0ccc1ce41f05b792425f3fb9c158083a6db1928102b69608",
    "source_references": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 109; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000103",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000103",
    "preferred_label": "Quantitative Bias Analysis Robustness",
    "normalized_label": "quantitative_bias_analysis_robustness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100004",
    "category_label": "Causal Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100004",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of quantitative bias analysis robustness.",
    "what_it_measures": "Assesses quantitative bias analysis robustness using evidence appropriate to causal inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in quantitative bias analysis robustness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "related_frameworks_source": "ROBINS-I; ROBINS-E; GRADE; STROBE; ICH E9",
    "closely_related_metrics_source": "Selection-on-Survival Bias Risk; E-value Strength; Assumption Sensitivity",
    "common_misinterpretations": "Treating quantitative bias analysis robustness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "domain_applicability": "Causal Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000103",
    "api_endpoint_template": "/v1/metrics/BEMO:2000103/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000103_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 110,
    "source_record_hash": "7ee1bd197cfd8211ed7ac785b0e49ec8e73324814e415213789e479477f73c74",
    "source_references": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 110; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000104",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000104",
    "preferred_label": "Residual Confounding Risk",
    "normalized_label": "residual_confounding_risk",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100004",
    "category_label": "Causal Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100004",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that residual confounding introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses residual confounding risk using evidence appropriate to causal inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in residual confounding risk can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Directed acyclic graphs; design emulation; balance diagnostics; negative controls; quantitative bias analysis; sensitivity and falsification analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "related_frameworks_source": "ROBINS-I; ROBINS-E; GRADE; STROBE; ICH E9",
    "closely_related_metrics_source": "Confounding Risk; Unmeasured Confounding Sensitivity; Exchangeability Plausibility",
    "common_misinterpretations": "Treating residual confounding risk as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "domain_applicability": "Causal Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000104",
    "api_endpoint_template": "/v1/metrics/BEMO:2000104/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000104_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 111,
    "source_record_hash": "fef3c7d8a6ff0d0d4088a08abb2cfe7420127e6170b4998b7b5ce06d44124e81",
    "source_references": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 111; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000105",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000105",
    "preferred_label": "Reverse-Causation Risk",
    "normalized_label": "reverse_causation_risk",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100004",
    "category_label": "Causal Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100004",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that reverse-causation introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses reverse-causation risk using evidence appropriate to causal inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in reverse-causation risk can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "related_frameworks_source": "ROBINS-I; ROBINS-E; GRADE; STROBE; ICH E9",
    "closely_related_metrics_source": "Immortal-Time Bias Risk; Selection-on-Survival Bias Risk; Quantitative Bias Analysis Robustness",
    "common_misinterpretations": "Treating reverse-causation risk as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "domain_applicability": "Causal Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000105",
    "api_endpoint_template": "/v1/metrics/BEMO:2000105/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000105_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 112,
    "source_record_hash": "17fc4b74f3434a4ae22f908b09530b9a1be33f82af499c89239235d78d7e1375",
    "source_references": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 112; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000106",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000106",
    "preferred_label": "Selection-on-Survival Bias Risk",
    "normalized_label": "selection_on_survival_bias_risk",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100004",
    "category_label": "Causal Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100004",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that selection-on-survival bias introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses selection-on-survival bias risk using evidence appropriate to causal inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in selection-on-survival bias risk can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "related_frameworks_source": "ROBINS-I; ROBINS-E; GRADE; STROBE; ICH E9",
    "closely_related_metrics_source": "Reverse-Causation Risk; Quantitative Bias Analysis Robustness; E-value Strength",
    "common_misinterpretations": "Treating selection-on-survival bias risk as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "domain_applicability": "Causal Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000106",
    "api_endpoint_template": "/v1/metrics/BEMO:2000106/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000106_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 113,
    "source_record_hash": "ba5e2bde29a386ccb9cae3afe1f1c9476a350f65371bc1aebd58a3579e6e702c",
    "source_references": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 113; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000107",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000107",
    "preferred_label": "Target Trial Emulation Fidelity",
    "normalized_label": "target_trial_emulation_fidelity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100004",
    "category_label": "Causal Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100004",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of target trial emulation fidelity.",
    "what_it_measures": "Assesses target trial emulation fidelity using evidence appropriate to causal inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in target trial emulation fidelity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "related_frameworks_source": "ROBINS-I; ROBINS-E; GRADE; STROBE; ICH E9",
    "closely_related_metrics_source": "Causal Contrast Clarity; Instrument Validity; Negative-Control Validation",
    "common_misinterpretations": "Treating target trial emulation fidelity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "domain_applicability": "Causal Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000107",
    "api_endpoint_template": "/v1/metrics/BEMO:2000107/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000107_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 114,
    "source_record_hash": "7a907a8dc4fe2c40df0aa3c333c85c8e7231c1e33d26321171335bcd3464b6a6",
    "source_references": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 114; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000108",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000108",
    "preferred_label": "Time-Varying Confounding Control",
    "normalized_label": "time_varying_confounding_control",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100004",
    "category_label": "Causal Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100004",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of time-varying confounding control.",
    "what_it_measures": "Assesses time-varying confounding control using evidence appropriate to causal inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in time-varying confounding control can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Directed acyclic graphs; design emulation; balance diagnostics; negative controls; quantitative bias analysis; sensitivity and falsification analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "related_frameworks_source": "ROBINS-I; ROBINS-E; GRADE; STROBE; ICH E9",
    "closely_related_metrics_source": "Collider Bias Risk; Immortal-Time Bias Risk; Reverse-Causation Risk",
    "common_misinterpretations": "Treating time-varying confounding control as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "domain_applicability": "Causal Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000108",
    "api_endpoint_template": "/v1/metrics/BEMO:2000108/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000108_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 115,
    "source_record_hash": "f46690f0cea7611ea5bb0e9a0e5c1b90d25ecad9c8f28f3083cc2a71b53ce7f0",
    "source_references": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 115; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000109",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000109",
    "preferred_label": "Unmeasured Confounding Sensitivity",
    "normalized_label": "unmeasured_confounding_sensitivity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100004",
    "category_label": "Causal Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100004",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of unmeasured confounding sensitivity.",
    "what_it_measures": "Assesses unmeasured confounding sensitivity using evidence appropriate to causal inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in unmeasured confounding sensitivity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified threshold; valid reference standard; complete 2×2 classification; confidence intervals; spectrum and prevalence assessment.",
    "methods_of_assessment": "Directed acyclic graphs; design emulation; balance diagnostics; negative controls; quantitative bias analysis; sensitivity and falsification analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "related_frameworks_source": "ROBINS-I; ROBINS-E; GRADE; STROBE; ICH E9",
    "closely_related_metrics_source": "Residual Confounding Risk; Exchangeability Plausibility; Positivity Adequacy",
    "common_misinterpretations": "Treating unmeasured confounding sensitivity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized and observational etiologic studies, natural experiments, target-trial emulations",
    "domain_applicability": "Causal Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000109",
    "api_endpoint_template": "/v1/metrics/BEMO:2000109/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000109_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 116,
    "source_record_hash": "50677da95ed69c14f1f1ec5786cb5c4d590d6e339c1a13fdedfd18d811ffc8f4",
    "source_references": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 116; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.gradeworkinggroup.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000110",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000110",
    "preferred_label": "Area Under the Receiver Operating Characteristic Curve",
    "normalized_label": "area_under_the_receiver_operating_characteristic_curve",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100005",
    "category_label": "Diagnostic and Prognostic Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100005",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of area under the receiver operating characteristic curve.",
    "what_it_measures": "Assesses area under the receiver operating characteristic curve using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in area under the receiver operating characteristic curve can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "related_frameworks_source": "QUADAS-2; STARD; TRIPOD; REMARK",
    "closely_related_metrics_source": "Diagnostic Odds Ratio; Partial Area Under the Receiver Operating Characteristic Curve; Threshold Validity",
    "common_misinterpretations": "Treating area under the receiver operating characteristic curve as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "domain_applicability": "Diagnostic and Prognostic Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000110",
    "api_endpoint_template": "/v1/metrics/BEMO:2000110/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000110_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 117,
    "source_record_hash": "5c4feaae4c2a565042108ac4cb807678f9be09f3e84e62f596afd3338e3ceec6",
    "source_references": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 117; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000111",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000111",
    "preferred_label": "Calibration Slope",
    "normalized_label": "calibration_slope",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100005",
    "category_label": "Diagnostic and Prognostic Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100005",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of calibration slope.",
    "what_it_measures": "Assesses calibration slope using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in calibration slope can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "related_frameworks_source": "QUADAS-2; STARD; TRIPOD; REMARK",
    "closely_related_metrics_source": "Prognostic Calibration; Calibration-in-the-Large; Observed-to-Expected Ratio",
    "common_misinterpretations": "Treating calibration slope as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "domain_applicability": "Diagnostic and Prognostic Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000111",
    "api_endpoint_template": "/v1/metrics/BEMO:2000111/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000111_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 118,
    "source_record_hash": "44bfcfec74d2b98de3507998b5e63f6506912c93210fea4df7a678aed4417a75",
    "source_references": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 118; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000112",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000112",
    "preferred_label": "Calibration-in-the-Large",
    "normalized_label": "calibration_in_the_large",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100005",
    "category_label": "Diagnostic and Prognostic Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100005",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of calibration-in-the-large.",
    "what_it_measures": "Assesses calibration-in-the-large using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in calibration-in-the-large can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "related_frameworks_source": "QUADAS-2; STARD; TRIPOD; REMARK",
    "closely_related_metrics_source": "Calibration Slope; Observed-to-Expected Ratio; Prognostic Added Value",
    "common_misinterpretations": "Treating calibration-in-the-large as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "domain_applicability": "Diagnostic and Prognostic Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000112",
    "api_endpoint_template": "/v1/metrics/BEMO:2000112/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000112_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 119,
    "source_record_hash": "4a117ceb82993be69cf387d42f6626e25d4ff682e98eb458d01d55a60ca6f29d",
    "source_references": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 119; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000113",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000113",
    "preferred_label": "Comparative Test Accuracy",
    "normalized_label": "comparative_test_accuracy",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100005",
    "category_label": "Diagnostic and Prognostic Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100005",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The closeness of comparative test to the accepted reference or true value.",
    "what_it_measures": "Assesses comparative test accuracy using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in comparative test accuracy can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "related_frameworks_source": "QUADAS-2; STARD; TRIPOD; REMARK",
    "closely_related_metrics_source": "Test-Timing Appropriateness; Incremental Diagnostic Value; Reclassification Improvement",
    "common_misinterpretations": "Treating comparative test accuracy as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "domain_applicability": "Diagnostic and Prognostic Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000113",
    "api_endpoint_template": "/v1/metrics/BEMO:2000113/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000113_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 120,
    "source_record_hash": "01f4b65430acfaca391e550bb1550450d424a1dd47aebe4ed0f6dd9d60fe28ab",
    "source_references": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 120; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000114",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000114",
    "preferred_label": "Competing-Risk Model Validity",
    "normalized_label": "competing_risk_model_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100005",
    "category_label": "Diagnostic and Prognostic Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100005",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that competing-risk model validity introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses competing-risk model validity using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in competing-risk model validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "related_frameworks_source": "QUADAS-2; STARD; TRIPOD; REMARK",
    "closely_related_metrics_source": "Time-Dependent Discrimination",
    "common_misinterpretations": "Treating competing-risk model validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "domain_applicability": "Diagnostic and Prognostic Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000114",
    "api_endpoint_template": "/v1/metrics/BEMO:2000114/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000114_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 121,
    "source_record_hash": "6f322698057cc9561b413498181b8f2503720420a935d144d2173ae5298a3b2f",
    "source_references": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 121; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000115",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000115",
    "preferred_label": "Diagnostic Odds Ratio",
    "normalized_label": "diagnostic_odds_ratio",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100005",
    "category_label": "Diagnostic and Prognostic Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100005",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of diagnostic odds ratio.",
    "what_it_measures": "Assesses diagnostic odds ratio using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in diagnostic odds ratio can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Two-by-two tables; binomial confidence intervals; hierarchical diagnostic meta-analysis; threshold and prevalence analyses.",
    "units_or_scale_source": "Ratio scale; null typically 1",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "related_frameworks_source": "QUADAS-2; STARD; TRIPOD; REMARK",
    "closely_related_metrics_source": "Negative Likelihood Ratio; Area Under the Receiver Operating Characteristic Curve; Partial Area Under the Receiver Operating Characteristic Curve",
    "common_misinterpretations": "Treating diagnostic odds ratio as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RatioScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ratio scale; null typically 1",
    "minimum_value": 0.0,
    "maximum_value": null,
    "null_value": 1.0,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeRatioComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator; the null value is typically 1 where scientifically applicable",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator != 0\"],\"null_value\":1}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "confidence_level; stratum",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Not generally required unless converted to a probability or score.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "domain_applicability": "Diagnostic and Prognostic Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "ratio estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000115",
    "api_endpoint_template": "/v1/metrics/BEMO:2000115/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000115_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 122,
    "source_record_hash": "a903f03627bce43e756f3c1d10c27c552a53bce0346a40196ea1cd72afe63de0",
    "source_references": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 122; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000116",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000116",
    "preferred_label": "Diagnostic Sensitivity",
    "normalized_label": "diagnostic_sensitivity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100005",
    "category_label": "Diagnostic and Prognostic Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100005",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of diagnostic sensitivity.",
    "what_it_measures": "Assesses diagnostic sensitivity using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in diagnostic sensitivity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified threshold; valid reference standard; complete 2×2 classification; confidence intervals; spectrum and prevalence assessment.",
    "methods_of_assessment": "Two-by-two tables; binomial confidence intervals; hierarchical diagnostic meta-analysis; threshold and prevalence analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "related_frameworks_source": "QUADAS-2; STARD; TRIPOD; REMARK",
    "closely_related_metrics_source": "Diagnostic Specificity; Positive Predictive Value",
    "common_misinterpretations": "Treating diagnostic sensitivity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "domain_applicability": "Diagnostic and Prognostic Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000116",
    "api_endpoint_template": "/v1/metrics/BEMO:2000116/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000116_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 123,
    "source_record_hash": "4ea75714eea731a1e4644a00db0476f8628bf028934f92bd9e4029ee31ddf173",
    "source_references": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 123; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000117",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000117",
    "preferred_label": "Diagnostic Specificity",
    "normalized_label": "diagnostic_specificity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100005",
    "category_label": "Diagnostic and Prognostic Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100005",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of diagnostic specificity.",
    "what_it_measures": "Assesses diagnostic specificity using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in diagnostic specificity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified threshold; valid reference standard; complete 2×2 classification; confidence intervals; spectrum and prevalence assessment.",
    "methods_of_assessment": "Two-by-two tables; binomial confidence intervals; hierarchical diagnostic meta-analysis; threshold and prevalence analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "related_frameworks_source": "QUADAS-2; STARD; TRIPOD; REMARK",
    "closely_related_metrics_source": "Diagnostic Sensitivity; Positive Predictive Value; Negative Predictive Value",
    "common_misinterpretations": "Treating diagnostic specificity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "domain_applicability": "Diagnostic and Prognostic Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000117",
    "api_endpoint_template": "/v1/metrics/BEMO:2000117/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000117_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 124,
    "source_record_hash": "14be8f0b88f11902e6b1562a38b9cb710840858fc59f748048f96b74c8f6c2b2",
    "source_references": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 124; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000118",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000118",
    "preferred_label": "Differential Verification Bias Risk",
    "normalized_label": "differential_verification_bias_risk",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100005",
    "category_label": "Diagnostic and Prognostic Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100005",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that differential verification bias introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses differential verification bias risk using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in differential verification bias risk can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "related_frameworks_source": "QUADAS-2; STARD; TRIPOD; REMARK",
    "closely_related_metrics_source": "Verification Bias Risk; Incorporation Bias Risk; Patient Flow Integrity",
    "common_misinterpretations": "Treating differential verification bias risk as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "domain_applicability": "Diagnostic and Prognostic Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000118",
    "api_endpoint_template": "/v1/metrics/BEMO:2000118/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000118_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 125,
    "source_record_hash": "2805e0d0838d99254f4675a5517e72c35cb3e1cb875fbc214edb03376568c858",
    "source_references": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 125; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000119",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000119",
    "preferred_label": "Incorporation Bias Risk",
    "normalized_label": "incorporation_bias_risk",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100005",
    "category_label": "Diagnostic and Prognostic Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100005",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that incorporation bias introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses incorporation bias risk using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in incorporation bias risk can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "related_frameworks_source": "QUADAS-2; STARD; TRIPOD; REMARK",
    "closely_related_metrics_source": "Differential Verification Bias Risk; Patient Flow Integrity; Test-Timing Appropriateness",
    "common_misinterpretations": "Treating incorporation bias risk as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "domain_applicability": "Diagnostic and Prognostic Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000119",
    "api_endpoint_template": "/v1/metrics/BEMO:2000119/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000119_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 126,
    "source_record_hash": "00ceeb2a9486ba76c68ad0f07ad3fe11fadf573e3b3b3fb37898281142b34a91",
    "source_references": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 126; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000120",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000120",
    "preferred_label": "Incremental Diagnostic Value",
    "normalized_label": "incremental_diagnostic_value",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100005",
    "category_label": "Diagnostic and Prognostic Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100005",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of incremental diagnostic value.",
    "what_it_measures": "Assesses incremental diagnostic value using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in incremental diagnostic value can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "related_frameworks_source": "QUADAS-2; STARD; TRIPOD; REMARK",
    "closely_related_metrics_source": "Comparative Test Accuracy; Reclassification Improvement; Prognostic Discrimination",
    "common_misinterpretations": "Treating incremental diagnostic value as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "domain_applicability": "Diagnostic and Prognostic Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000120",
    "api_endpoint_template": "/v1/metrics/BEMO:2000120/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000120_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 127,
    "source_record_hash": "8c0d8dc6983b3100a525f45a2c3c327af7d21cf2d155dc05a19b99e0d7f43578",
    "source_references": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 127; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000121",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000121",
    "preferred_label": "Index-Test Blinding",
    "normalized_label": "index_test_blinding",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100005",
    "category_label": "Diagnostic and Prognostic Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100005",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of index-test blinding.",
    "what_it_measures": "Assesses index-test blinding using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in index-test blinding can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "related_frameworks_source": "QUADAS-2; STARD; TRIPOD; REMARK",
    "closely_related_metrics_source": "Reference Standard Validity; Verification Bias Risk; Differential Verification Bias Risk",
    "common_misinterpretations": "Treating index-test blinding as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "domain_applicability": "Diagnostic and Prognostic Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000121",
    "api_endpoint_template": "/v1/metrics/BEMO:2000121/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000121_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 128,
    "source_record_hash": "3bc623a30f8cb3956f6d71196888c1021137e72c87604513c9fc1e352f98bb4c",
    "source_references": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 128; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000122",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000122",
    "preferred_label": "Negative Likelihood Ratio",
    "normalized_label": "negative_likelihood_ratio",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100005",
    "category_label": "Diagnostic and Prognostic Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100005",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of negative likelihood ratio.",
    "what_it_measures": "Assesses negative likelihood ratio using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in negative likelihood ratio can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified threshold; valid reference standard; complete 2×2 classification; confidence intervals; spectrum and prevalence assessment.",
    "methods_of_assessment": "Two-by-two tables; binomial confidence intervals; hierarchical diagnostic meta-analysis; threshold and prevalence analyses.",
    "units_or_scale_source": "Ratio scale; null typically 1",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "related_frameworks_source": "QUADAS-2; STARD; TRIPOD; REMARK",
    "closely_related_metrics_source": "Positive Likelihood Ratio; Diagnostic Odds Ratio; Area Under the Receiver Operating Characteristic Curve",
    "common_misinterpretations": "Treating negative likelihood ratio as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RatioScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ratio scale; null typically 1",
    "minimum_value": 0.0,
    "maximum_value": null,
    "null_value": 1.0,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeRatioComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator; the null value is typically 1 where scientifically applicable",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator != 0\"],\"null_value\":1}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "confidence_level; stratum",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Not generally required unless converted to a probability or score.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "domain_applicability": "Diagnostic and Prognostic Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "ratio estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000122",
    "api_endpoint_template": "/v1/metrics/BEMO:2000122/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000122_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 129,
    "source_record_hash": "6dc29889e79017542636c8b841aff4c0f5947b19dec51307e00a9c51cdc593cc",
    "source_references": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 129; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000123",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000123",
    "preferred_label": "Negative Predictive Value",
    "normalized_label": "negative_predictive_value",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100005",
    "category_label": "Diagnostic and Prognostic Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100005",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of negative predictive value.",
    "what_it_measures": "Assesses negative predictive value using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in negative predictive value can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified threshold; valid reference standard; complete 2×2 classification; confidence intervals; spectrum and prevalence assessment.",
    "methods_of_assessment": "Two-by-two tables; binomial confidence intervals; hierarchical diagnostic meta-analysis; threshold and prevalence analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "related_frameworks_source": "QUADAS-2; STARD; TRIPOD; REMARK",
    "closely_related_metrics_source": "Positive Predictive Value; Positive Likelihood Ratio; Negative Likelihood Ratio",
    "common_misinterpretations": "Treating negative predictive value as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "domain_applicability": "Diagnostic and Prognostic Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000123",
    "api_endpoint_template": "/v1/metrics/BEMO:2000123/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000123_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 130,
    "source_record_hash": "9f42e5362ad2e55445a028ec6d3cc9c062886d8c9272f983b0c1acec345502f7",
    "source_references": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 130; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000124",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000124",
    "preferred_label": "Observed-to-Expected Ratio",
    "normalized_label": "observed_to_expected_ratio",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100005",
    "category_label": "Diagnostic and Prognostic Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100005",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of observed-to-expected ratio.",
    "what_it_measures": "Assesses observed-to-expected ratio using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in observed-to-expected ratio can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "related_frameworks_source": "QUADAS-2; STARD; TRIPOD; REMARK",
    "closely_related_metrics_source": "Calibration-in-the-Large; Prognostic Added Value; Prognostic Transportability",
    "common_misinterpretations": "Treating observed-to-expected ratio as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "domain_applicability": "Diagnostic and Prognostic Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000124",
    "api_endpoint_template": "/v1/metrics/BEMO:2000124/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000124_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 131,
    "source_record_hash": "cdf33871a90f7426da799fbf8148672bff9e925c7981ff58372c39511bd4050e",
    "source_references": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 131; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000125",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000125",
    "preferred_label": "Partial Area Under the Receiver Operating Characteristic Curve",
    "normalized_label": "partial_area_under_the_receiver_operating_characteristic_curve",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100005",
    "category_label": "Diagnostic and Prognostic Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100005",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of partial area under the receiver operating characteristic curve.",
    "what_it_measures": "Assesses partial area under the receiver operating characteristic curve using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in partial area under the receiver operating characteristic curve can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "related_frameworks_source": "QUADAS-2; STARD; TRIPOD; REMARK",
    "closely_related_metrics_source": "Area Under the Receiver Operating Characteristic Curve; Threshold Validity; Reference Standard Validity",
    "common_misinterpretations": "Treating partial area under the receiver operating characteristic curve as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "domain_applicability": "Diagnostic and Prognostic Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000125",
    "api_endpoint_template": "/v1/metrics/BEMO:2000125/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000125_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 132,
    "source_record_hash": "79f6b607e0d7504f46e1d3842fa8966ae929db7058236a6b4ed553277ad444b5",
    "source_references": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 132; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000126",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000126",
    "preferred_label": "Patient Flow Integrity",
    "normalized_label": "patient_flow_integrity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100005",
    "category_label": "Diagnostic and Prognostic Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100005",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of patient flow integrity.",
    "what_it_measures": "Assesses patient flow integrity using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in patient flow integrity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "related_frameworks_source": "QUADAS-2; STARD; TRIPOD; REMARK",
    "closely_related_metrics_source": "Incorporation Bias Risk; Test-Timing Appropriateness; Comparative Test Accuracy",
    "common_misinterpretations": "Treating patient flow integrity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "domain_applicability": "Diagnostic and Prognostic Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000126",
    "api_endpoint_template": "/v1/metrics/BEMO:2000126/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000126_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 133,
    "source_record_hash": "67544e05c38d184f5e9fa9830136b1408e7835e115b1fa9c54147ad65e14b99c",
    "source_references": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 133; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000127",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000127",
    "preferred_label": "Positive Likelihood Ratio",
    "normalized_label": "positive_likelihood_ratio",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100005",
    "category_label": "Diagnostic and Prognostic Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100005",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of positive likelihood ratio.",
    "what_it_measures": "Assesses positive likelihood ratio using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in positive likelihood ratio can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified threshold; valid reference standard; complete 2×2 classification; confidence intervals; spectrum and prevalence assessment.",
    "methods_of_assessment": "Two-by-two tables; binomial confidence intervals; hierarchical diagnostic meta-analysis; threshold and prevalence analyses.",
    "units_or_scale_source": "Ratio scale; null typically 1",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "related_frameworks_source": "QUADAS-2; STARD; TRIPOD; REMARK",
    "closely_related_metrics_source": "Negative Predictive Value; Negative Likelihood Ratio; Diagnostic Odds Ratio",
    "common_misinterpretations": "Treating positive likelihood ratio as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RatioScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ratio scale; null typically 1",
    "minimum_value": 0.0,
    "maximum_value": null,
    "null_value": 1.0,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeRatioComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator; the null value is typically 1 where scientifically applicable",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator != 0\"],\"null_value\":1}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "confidence_level; stratum",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Not generally required unless converted to a probability or score.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "domain_applicability": "Diagnostic and Prognostic Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "ratio estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000127",
    "api_endpoint_template": "/v1/metrics/BEMO:2000127/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000127_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 134,
    "source_record_hash": "65ab6bc3c7bfa89dbab942e4977888e1ec5d3ea554c360ceffa76f4daab1fd7e",
    "source_references": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 134; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000128",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000128",
    "preferred_label": "Positive Predictive Value",
    "normalized_label": "positive_predictive_value",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100005",
    "category_label": "Diagnostic and Prognostic Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100005",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of positive predictive value.",
    "what_it_measures": "Assesses positive predictive value using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in positive predictive value can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified threshold; valid reference standard; complete 2×2 classification; confidence intervals; spectrum and prevalence assessment.",
    "methods_of_assessment": "Two-by-two tables; binomial confidence intervals; hierarchical diagnostic meta-analysis; threshold and prevalence analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "related_frameworks_source": "QUADAS-2; STARD; TRIPOD; REMARK",
    "closely_related_metrics_source": "Diagnostic Specificity; Negative Predictive Value; Positive Likelihood Ratio",
    "common_misinterpretations": "Treating positive predictive value as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "domain_applicability": "Diagnostic and Prognostic Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000128",
    "api_endpoint_template": "/v1/metrics/BEMO:2000128/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000128_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 135,
    "source_record_hash": "89034784369de0142956f172eb3ca87ccad9b4cc69ac8a45b8a92adf9cc1731f",
    "source_references": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 135; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000129",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000129",
    "preferred_label": "Prognostic Added Value",
    "normalized_label": "prognostic_added_value",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100005",
    "category_label": "Diagnostic and Prognostic Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100005",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of prognostic added value.",
    "what_it_measures": "Assesses prognostic added value using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in prognostic added value can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "related_frameworks_source": "QUADAS-2; STARD; TRIPOD; REMARK",
    "closely_related_metrics_source": "Observed-to-Expected Ratio; Prognostic Transportability; Time-Dependent Discrimination",
    "common_misinterpretations": "Treating prognostic added value as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "domain_applicability": "Diagnostic and Prognostic Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000129",
    "api_endpoint_template": "/v1/metrics/BEMO:2000129/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000129_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 136,
    "source_record_hash": "6a8e54c8d71bbaa2bc8361d6fc19eb1f50b8f4acd2b6d09e2b648f2337fa9298",
    "source_references": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 136; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000130",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000130",
    "preferred_label": "Prognostic Calibration",
    "normalized_label": "prognostic_calibration",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100005",
    "category_label": "Diagnostic and Prognostic Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100005",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of prognostic calibration.",
    "what_it_measures": "Assesses prognostic calibration using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in prognostic calibration can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "related_frameworks_source": "QUADAS-2; STARD; TRIPOD; REMARK",
    "closely_related_metrics_source": "Prognostic Discrimination; Calibration Slope; Calibration-in-the-Large",
    "common_misinterpretations": "Treating prognostic calibration as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "domain_applicability": "Diagnostic and Prognostic Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000130",
    "api_endpoint_template": "/v1/metrics/BEMO:2000130/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000130_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
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    "source_references": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 137; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000131",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000131",
    "preferred_label": "Prognostic Discrimination",
    "normalized_label": "prognostic_discrimination",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100005",
    "category_label": "Diagnostic and Prognostic Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100005",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of prognostic discrimination.",
    "what_it_measures": "Assesses prognostic discrimination using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in prognostic discrimination can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "related_frameworks_source": "QUADAS-2; STARD; TRIPOD; REMARK",
    "closely_related_metrics_source": "Reclassification Improvement; Prognostic Calibration; Calibration Slope",
    "common_misinterpretations": "Treating prognostic discrimination as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "domain_applicability": "Diagnostic and Prognostic Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000131",
    "api_endpoint_template": "/v1/metrics/BEMO:2000131/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000131_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
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    "source_references": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 138; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000132",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000132",
    "preferred_label": "Prognostic Transportability",
    "normalized_label": "prognostic_transportability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100005",
    "category_label": "Diagnostic and Prognostic Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100005",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of prognostic transportability.",
    "what_it_measures": "Assesses prognostic transportability using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in prognostic transportability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "related_frameworks_source": "QUADAS-2; STARD; TRIPOD; REMARK",
    "closely_related_metrics_source": "Prognostic Added Value; Time-Dependent Discrimination; Competing-Risk Model Validity",
    "common_misinterpretations": "Treating prognostic transportability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "domain_applicability": "Diagnostic and Prognostic Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000132",
    "api_endpoint_template": "/v1/metrics/BEMO:2000132/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000132_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
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    "source_record_hash": "c2720768cdf2be8ed6a3b935c205e9cb522ea1c958d036e680eee5e7cba4038e",
    "source_references": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 139; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000133",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000133",
    "preferred_label": "Reclassification Improvement",
    "normalized_label": "reclassification_improvement",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100005",
    "category_label": "Diagnostic and Prognostic Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100005",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of reclassification improvement.",
    "what_it_measures": "Assesses reclassification improvement using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in reclassification improvement can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "related_frameworks_source": "QUADAS-2; STARD; TRIPOD; REMARK",
    "closely_related_metrics_source": "Incremental Diagnostic Value; Prognostic Discrimination; Prognostic Calibration",
    "common_misinterpretations": "Treating reclassification improvement as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "domain_applicability": "Diagnostic and Prognostic Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000133",
    "api_endpoint_template": "/v1/metrics/BEMO:2000133/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000133_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 140,
    "source_record_hash": "74d83029c18dff3247c8fb9baae1d6aba52c9b7328d218dd0210458cbd5ad7d5",
    "source_references": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 140; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000134",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000134",
    "preferred_label": "Reference Standard Validity",
    "normalized_label": "reference_standard_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100005",
    "category_label": "Diagnostic and Prognostic Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100005",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which reference standard supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses reference standard validity using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in reference standard validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "related_frameworks_source": "QUADAS-2; STARD; TRIPOD; REMARK",
    "closely_related_metrics_source": "Threshold Validity; Index-Test Blinding; Verification Bias Risk",
    "common_misinterpretations": "Treating reference standard validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "domain_applicability": "Diagnostic and Prognostic Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000134",
    "api_endpoint_template": "/v1/metrics/BEMO:2000134/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000134_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 141,
    "source_record_hash": "3bd12b9aed8e6e227ec8b1e5082fc9060b988babbc4204f8a360bb7503e6ad49",
    "source_references": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 141; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000135",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000135",
    "preferred_label": "Test-Timing Appropriateness",
    "normalized_label": "test_timing_appropriateness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100005",
    "category_label": "Diagnostic and Prognostic Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100005",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which test-timing is sufficient and fit for the stated biomedical inference.",
    "what_it_measures": "Assesses test-timing appropriateness using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in test-timing appropriateness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "related_frameworks_source": "QUADAS-2; STARD; TRIPOD; REMARK",
    "closely_related_metrics_source": "Patient Flow Integrity; Comparative Test Accuracy; Incremental Diagnostic Value",
    "common_misinterpretations": "Treating test-timing appropriateness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "domain_applicability": "Diagnostic and Prognostic Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000135",
    "api_endpoint_template": "/v1/metrics/BEMO:2000135/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000135_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 142,
    "source_record_hash": "ffb2707e3bed89aca5f5c790dc5a9b0312e89c5a1dba27ebac908e4597a355bd",
    "source_references": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 142; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000136",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000136",
    "preferred_label": "Threshold Validity",
    "normalized_label": "threshold_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100005",
    "category_label": "Diagnostic and Prognostic Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100005",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which threshold supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses threshold validity using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in threshold validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "related_frameworks_source": "QUADAS-2; STARD; TRIPOD; REMARK",
    "closely_related_metrics_source": "Partial Area Under the Receiver Operating Characteristic Curve; Reference Standard Validity; Index-Test Blinding",
    "common_misinterpretations": "Treating threshold validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "domain_applicability": "Diagnostic and Prognostic Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000136",
    "api_endpoint_template": "/v1/metrics/BEMO:2000136/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000136_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 143,
    "source_record_hash": "c27bfe6217acf4b748aeb85aa4e9c4176c8256e12b7c61ff84a201b6fd374c82",
    "source_references": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 143; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000137",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000137",
    "preferred_label": "Time-Dependent Discrimination",
    "normalized_label": "time_dependent_discrimination",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100005",
    "category_label": "Diagnostic and Prognostic Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100005",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of time-dependent discrimination.",
    "what_it_measures": "Assesses time-dependent discrimination using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in time-dependent discrimination can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "related_frameworks_source": "QUADAS-2; STARD; TRIPOD; REMARK",
    "closely_related_metrics_source": "Prognostic Transportability; Competing-Risk Model Validity",
    "common_misinterpretations": "Treating time-dependent discrimination as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "domain_applicability": "Diagnostic and Prognostic Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000137",
    "api_endpoint_template": "/v1/metrics/BEMO:2000137/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000137_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 144,
    "source_record_hash": "5232bfe9f1dc1ddd88662ddb65a550d0d1fc5338bb4a530ed1072ed6078116bf",
    "source_references": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 144; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000138",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000138",
    "preferred_label": "Verification Bias Risk",
    "normalized_label": "verification_bias_risk",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100005",
    "category_label": "Diagnostic and Prognostic Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100005",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that verification bias introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses verification bias risk using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in verification bias risk can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "related_frameworks_source": "QUADAS-2; STARD; TRIPOD; REMARK",
    "closely_related_metrics_source": "Index-Test Blinding; Differential Verification Bias Risk; Incorporation Bias Risk",
    "common_misinterpretations": "Treating verification bias risk as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies",
    "domain_applicability": "Diagnostic and Prognostic Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000138",
    "api_endpoint_template": "/v1/metrics/BEMO:2000138/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000138_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 145,
    "source_record_hash": "2f165758b70b1e482bfb8517e1a69a7d4e05ba84cd41dc36c2f346f991371034",
    "source_references": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 145; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000139",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000139",
    "preferred_label": "Between-Study Variance",
    "normalized_label": "between_study_variance",
    "abbreviation": "",
    "pillar_id": "BEMO:1000001",
    "pillar_label": "Evidence Synthesis and Certainty",
    "category_id": "BEMO:1100006",
    "category_label": "Evidence Certainty and Synthesis",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100006",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of between-study variance.",
    "what_it_measures": "Assesses between-study variance using evidence appropriate to evidence certainty and synthesis, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in between-study variance can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Forest plots; heterogeneity statistics; tau-squared; prediction intervals; funnel plots; regression or selection models; sensitivity analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "related_frameworks_source": "GRADE; PRISMA; AMSTAR 2; RoB",
    "closely_related_metrics_source": "Study Heterogeneity; Prediction Interval Adequacy; Cumulative Evidence Stability",
    "common_misinterpretations": "Treating between-study variance as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "domain_applicability": "Evidence Certainty and Synthesis",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000139",
    "api_endpoint_template": "/v1/metrics/BEMO:2000139/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000139_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 146,
    "source_record_hash": "167d33dabeef5837833710d7e97d42ff17e46ede74b98e0e88db46e921ff811e",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 146; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "obo_subset": "bemo_evidence_synthesis_and_certainty",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000140",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000140",
    "preferred_label": "Counterevidence Strength",
    "normalized_label": "counterevidence_strength",
    "abbreviation": "",
    "pillar_id": "BEMO:1000001",
    "pillar_label": "Evidence Synthesis and Certainty",
    "category_id": "BEMO:1100006",
    "category_label": "Evidence Certainty and Synthesis",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100006",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting counterevidence.",
    "what_it_measures": "Assesses counterevidence strength using evidence appropriate to evidence certainty and synthesis, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in counterevidence strength can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "related_frameworks_source": "GRADE; PRISMA; AMSTAR 2; RoB",
    "closely_related_metrics_source": "Evidence Triangulation Strength; Missing Evidence Risk; Publication Bias Risk",
    "common_misinterpretations": "Treating counterevidence strength as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "domain_applicability": "Evidence Certainty and Synthesis",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000140",
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    "json_schema_ref": "schemas/bemo-assessment.schema.json",
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    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 147,
    "source_record_hash": "d4c1d3bbceb7e86e058c678a7bbc386dd5980f93dcbc9a60ebc6c6d39231fcdb",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 147; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "obo_subset": "bemo_evidence_synthesis_and_certainty",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000141",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000141",
    "preferred_label": "Cumulative Evidence Stability",
    "normalized_label": "cumulative_evidence_stability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000001",
    "pillar_label": "Evidence Synthesis and Certainty",
    "category_id": "BEMO:1100006",
    "category_label": "Evidence Certainty and Synthesis",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100006",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of cumulative evidence stability.",
    "what_it_measures": "Assesses cumulative evidence stability using evidence appropriate to evidence certainty and synthesis, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in cumulative evidence stability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "related_frameworks_source": "GRADE; PRISMA; AMSTAR 2; RoB",
    "closely_related_metrics_source": "Prediction Interval Adequacy; Information Size Adequacy; Multiplicity-Adjusted Credibility",
    "common_misinterpretations": "Treating cumulative evidence stability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "domain_applicability": "Evidence Certainty and Synthesis",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000141",
    "api_endpoint_template": "/v1/metrics/BEMO:2000141/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000141_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 148,
    "source_record_hash": "e87943e84aae44a1eeb6300f5a52416f0528fe0f3bf76f40f0a2a4486c87ea6a",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 148; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "obo_subset": "bemo_evidence_synthesis_and_certainty",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000142",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000142",
    "preferred_label": "Evidence Coherence",
    "normalized_label": "evidence_coherence",
    "abbreviation": "",
    "pillar_id": "BEMO:1000001",
    "pillar_label": "Evidence Synthesis and Certainty",
    "category_id": "BEMO:1100006",
    "category_label": "Evidence Certainty and Synthesis",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100006",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of evidence coherence.",
    "what_it_measures": "Assesses evidence coherence using evidence appropriate to evidence certainty and synthesis, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in evidence coherence can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "related_frameworks_source": "GRADE; PRISMA; AMSTAR 2; RoB",
    "closely_related_metrics_source": "Evidence Precision; Evidence Consensus Strength; Evidence Sufficiency",
    "common_misinterpretations": "Treating evidence coherence as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "domain_applicability": "Evidence Certainty and Synthesis",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000142",
    "api_endpoint_template": "/v1/metrics/BEMO:2000142/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000142_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 149,
    "source_record_hash": "573628981de9da600edff4f13001018973ec4403d9ad58179a02f6958d0404dd",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 149; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "obo_subset": "bemo_evidence_synthesis_and_certainty",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000143",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000143",
    "preferred_label": "Evidence Completeness",
    "normalized_label": "evidence_completeness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000001",
    "pillar_label": "Evidence Synthesis and Certainty",
    "category_id": "BEMO:1100006",
    "category_label": "Evidence Certainty and Synthesis",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100006",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which all scientifically necessary components of evidence are present, documented, and evaluable.",
    "what_it_measures": "Assesses evidence completeness using evidence appropriate to evidence certainty and synthesis, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in evidence completeness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "related_frameworks_source": "GRADE; PRISMA; AMSTAR 2; RoB",
    "closely_related_metrics_source": "Evidence Sufficiency; Evidence Coverage; Evidence Freshness",
    "common_misinterpretations": "Treating evidence completeness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "domain_applicability": "Evidence Certainty and Synthesis",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000143",
    "api_endpoint_template": "/v1/metrics/BEMO:2000143/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000143_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 150,
    "source_record_hash": "263bd485141b0cc75ee285fb1989c667b83eb378666886a960ed5bd2a610f232",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 150; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "obo_subset": "bemo_evidence_synthesis_and_certainty",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000144",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000144",
    "preferred_label": "Evidence Confidence",
    "normalized_label": "evidence_confidence",
    "abbreviation": "",
    "pillar_id": "BEMO:1000001",
    "pillar_label": "Evidence Synthesis and Certainty",
    "category_id": "BEMO:1100006",
    "category_label": "Evidence Certainty and Synthesis",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100006",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The justified degree of certainty assigned to evidence given the quantity, quality, consistency, and limitations of supporting evidence.",
    "what_it_measures": "Assesses evidence confidence using evidence appropriate to evidence certainty and synthesis, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in evidence confidence can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "related_frameworks_source": "GRADE; PRISMA; AMSTAR 2; RoB",
    "closely_related_metrics_source": "Evidence Strength; Evidence Stability; Evidence Consistency",
    "common_misinterpretations": "Treating evidence confidence as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "domain_applicability": "Evidence Certainty and Synthesis",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000144",
    "api_endpoint_template": "/v1/metrics/BEMO:2000144/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000144_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 151,
    "source_record_hash": "a6abc5b380d07d44d4ec1e48b63cf0e3bf7299ab7264d6edcc898627f3bd0952",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 151; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "obo_subset": "bemo_evidence_synthesis_and_certainty",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000145",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000145",
    "preferred_label": "Evidence Consensus Strength",
    "normalized_label": "evidence_consensus_strength",
    "abbreviation": "",
    "pillar_id": "BEMO:1000001",
    "pillar_label": "Evidence Synthesis and Certainty",
    "category_id": "BEMO:1100006",
    "category_label": "Evidence Certainty and Synthesis",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100006",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting evidence consensus.",
    "what_it_measures": "Assesses evidence consensus strength using evidence appropriate to evidence certainty and synthesis, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in evidence consensus strength can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "related_frameworks_source": "GRADE; PRISMA; AMSTAR 2; RoB",
    "closely_related_metrics_source": "Evidence Coherence; Evidence Sufficiency; Evidence Completeness",
    "common_misinterpretations": "Treating evidence consensus strength as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "domain_applicability": "Evidence Certainty and Synthesis",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000145",
    "api_endpoint_template": "/v1/metrics/BEMO:2000145/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000145_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 152,
    "source_record_hash": "f207ed4da0508b76cb7e86f43fc62efc4861d327760c860608fc73ff3f4a6da8",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 152; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "obo_subset": "bemo_evidence_synthesis_and_certainty",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000146",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000146",
    "preferred_label": "Evidence Consistency",
    "normalized_label": "evidence_consistency",
    "abbreviation": "",
    "pillar_id": "BEMO:1000001",
    "pillar_label": "Evidence Synthesis and Certainty",
    "category_id": "BEMO:1100006",
    "category_label": "Evidence Certainty and Synthesis",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100006",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree of agreement in evidence across measurements, studies, methods, populations, or biological levels.",
    "what_it_measures": "Assesses evidence consistency using evidence appropriate to evidence certainty and synthesis, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in evidence consistency can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "related_frameworks_source": "GRADE; PRISMA; AMSTAR 2; RoB",
    "closely_related_metrics_source": "Evidence Stability; Evidence Directness; Evidence Precision",
    "common_misinterpretations": "Treating evidence consistency as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "domain_applicability": "Evidence Certainty and Synthesis",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000146",
    "api_endpoint_template": "/v1/metrics/BEMO:2000146/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000146_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 153,
    "source_record_hash": "f74a279906eee7e4453803727494ade321b94fc1d6196fb1882daae7f1abcf75",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 153; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "obo_subset": "bemo_evidence_synthesis_and_certainty",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000147",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000147",
    "preferred_label": "Evidence Coverage",
    "normalized_label": "evidence_coverage",
    "abbreviation": "",
    "pillar_id": "BEMO:1000001",
    "pillar_label": "Evidence Synthesis and Certainty",
    "category_id": "BEMO:1100006",
    "category_label": "Evidence Certainty and Synthesis",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100006",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The proportion and representativeness of the relevant evidence captured by the evidence or measurement process.",
    "what_it_measures": "Assesses evidence coverage using evidence appropriate to evidence certainty and synthesis, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in evidence coverage can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "related_frameworks_source": "GRADE; PRISMA; AMSTAR 2; RoB",
    "closely_related_metrics_source": "Evidence Completeness; Evidence Freshness; Evidence Robustness",
    "common_misinterpretations": "Treating evidence coverage as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "domain_applicability": "Evidence Certainty and Synthesis",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000147",
    "api_endpoint_template": "/v1/metrics/BEMO:2000147/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000147_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 154,
    "source_record_hash": "a64cee9a2114ea7d5580ea8d59eaef0691fce1d63dd3e4fd9f3d63e0dac86a3d",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 154; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "obo_subset": "bemo_evidence_synthesis_and_certainty",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000148",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000148",
    "preferred_label": "Evidence Directness",
    "normalized_label": "evidence_directness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000001",
    "pillar_label": "Evidence Synthesis and Certainty",
    "category_id": "BEMO:1100006",
    "category_label": "Evidence Certainty and Synthesis",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100006",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of evidence directness.",
    "what_it_measures": "Assesses evidence directness using evidence appropriate to evidence certainty and synthesis, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in evidence directness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "related_frameworks_source": "GRADE; PRISMA; AMSTAR 2; RoB",
    "closely_related_metrics_source": "Evidence Consistency; Evidence Precision; Evidence Coherence",
    "common_misinterpretations": "Treating evidence directness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "domain_applicability": "Evidence Certainty and Synthesis",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000148",
    "api_endpoint_template": "/v1/metrics/BEMO:2000148/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000148_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 155,
    "source_record_hash": "880de5f192c9dc60c14576e428f1c46fbdcda3180afe950bcde297920e65c6df",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 155; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "obo_subset": "bemo_evidence_synthesis_and_certainty",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000149",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000149",
    "preferred_label": "Evidence Freshness",
    "normalized_label": "evidence_freshness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000001",
    "pillar_label": "Evidence Synthesis and Certainty",
    "category_id": "BEMO:1100006",
    "category_label": "Evidence Certainty and Synthesis",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100006",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of evidence freshness.",
    "what_it_measures": "Assesses evidence freshness using evidence appropriate to evidence certainty and synthesis, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in evidence freshness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "related_frameworks_source": "GRADE; PRISMA; AMSTAR 2; RoB",
    "closely_related_metrics_source": "Evidence Coverage; Evidence Robustness; Evidence Triangulation Strength",
    "common_misinterpretations": "Treating evidence freshness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "domain_applicability": "Evidence Certainty and Synthesis",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000149",
    "api_endpoint_template": "/v1/metrics/BEMO:2000149/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000149_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 156,
    "source_record_hash": "2dc879dd1ad8ed3ebf228b83983e7de95e06b9c72131b584ccaa785f551eea2b",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 156; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "obo_subset": "bemo_evidence_synthesis_and_certainty",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000150",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000150",
    "preferred_label": "Evidence Precision",
    "normalized_label": "evidence_precision",
    "abbreviation": "",
    "pillar_id": "BEMO:1000001",
    "pillar_label": "Evidence Synthesis and Certainty",
    "category_id": "BEMO:1100006",
    "category_label": "Evidence Certainty and Synthesis",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100006",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The closeness of repeated estimates or measurements and the narrowness of uncertainty around evidence.",
    "what_it_measures": "Assesses evidence precision using evidence appropriate to evidence certainty and synthesis, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in evidence precision can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "related_frameworks_source": "GRADE; PRISMA; AMSTAR 2; RoB",
    "closely_related_metrics_source": "Evidence Directness; Evidence Coherence; Evidence Consensus Strength",
    "common_misinterpretations": "Treating evidence precision as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "domain_applicability": "Evidence Certainty and Synthesis",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000150",
    "api_endpoint_template": "/v1/metrics/BEMO:2000150/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000150_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 157,
    "source_record_hash": "fed12d9ff25f08fc6db399dc5bed2e8d719fc0db8bcefb33987a3ef3db40f55c",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 157; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "obo_subset": "bemo_evidence_synthesis_and_certainty",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000151",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000151",
    "preferred_label": "Evidence Quality",
    "normalized_label": "evidence_quality",
    "abbreviation": "",
    "pillar_id": "BEMO:1000001",
    "pillar_label": "Evidence Synthesis and Certainty",
    "category_id": "BEMO:1100006",
    "category_label": "Evidence Certainty and Synthesis",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100006",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of evidence quality.",
    "what_it_measures": "Assesses evidence quality using evidence appropriate to evidence certainty and synthesis, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in evidence quality can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "related_frameworks_source": "GRADE; PRISMA; AMSTAR 2; RoB",
    "closely_related_metrics_source": "Overall Evidence Certainty; Evidence Strength; Evidence Confidence",
    "common_misinterpretations": "Treating evidence quality as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "domain_applicability": "Evidence Certainty and Synthesis",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000151",
    "api_endpoint_template": "/v1/metrics/BEMO:2000151/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000151_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 158,
    "source_record_hash": "f4e08b1965ce7d1832ff4c5191f1e7298781d9bec3cb9a96c09198d6faaa1339",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 158; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "obo_subset": "bemo_evidence_synthesis_and_certainty",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000152",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000152",
    "preferred_label": "Evidence Robustness",
    "normalized_label": "evidence_robustness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000001",
    "pillar_label": "Evidence Synthesis and Certainty",
    "category_id": "BEMO:1100006",
    "category_label": "Evidence Certainty and Synthesis",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100006",
    "ontology_namespace": "BEMO",
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    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of evidence robustness.",
    "what_it_measures": "Assesses evidence robustness using evidence appropriate to evidence certainty and synthesis, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in evidence robustness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
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    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "related_frameworks_source": "GRADE; PRISMA; AMSTAR 2; RoB",
    "closely_related_metrics_source": "Evidence Freshness; Evidence Triangulation Strength; Counterevidence Strength",
    "common_misinterpretations": "Treating evidence robustness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
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    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "domain_applicability": "Evidence Certainty and Synthesis",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000152",
    "api_endpoint_template": "/v1/metrics/BEMO:2000152/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
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    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
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    "source_record_hash": "59315ce160586081fc3fd71f96646716829d26fde9e0a21aa0afec923b5083d6",
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    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 159; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "obo_subset": "bemo_evidence_synthesis_and_certainty",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
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    "metric_id": "BEMO:2000153",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000153",
    "preferred_label": "Evidence Stability",
    "normalized_label": "evidence_stability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000001",
    "pillar_label": "Evidence Synthesis and Certainty",
    "category_id": "BEMO:1100006",
    "category_label": "Evidence Certainty and Synthesis",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100006",
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    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of evidence stability.",
    "what_it_measures": "Assesses evidence stability using evidence appropriate to evidence certainty and synthesis, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in evidence stability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "related_frameworks_source": "GRADE; PRISMA; AMSTAR 2; RoB",
    "closely_related_metrics_source": "Evidence Confidence; Evidence Consistency; Evidence Directness",
    "common_misinterpretations": "Treating evidence stability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
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    "decision_thresholds": "",
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    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
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    "domain_applicability": "Evidence Certainty and Synthesis",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
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    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000153",
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    "provenance_model": "W3C PROV-O",
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    "source_sheet": "Biomedical Evidence Metrics",
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    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 160; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "obo_subset": "bemo_evidence_synthesis_and_certainty",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
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  {
    "metric_id": "BEMO:2000154",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000154",
    "preferred_label": "Evidence Strength",
    "normalized_label": "evidence_strength",
    "abbreviation": "",
    "pillar_id": "BEMO:1000001",
    "pillar_label": "Evidence Synthesis and Certainty",
    "category_id": "BEMO:1100006",
    "category_label": "Evidence Certainty and Synthesis",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100006",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
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    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting evidence.",
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    "why_it_matters": "Material weakness in evidence strength can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "related_frameworks_source": "GRADE; PRISMA; AMSTAR 2; RoB",
    "closely_related_metrics_source": "Evidence Quality; Evidence Confidence; Evidence Stability",
    "common_misinterpretations": "Treating evidence strength as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
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    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
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    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "domain_applicability": "Evidence Certainty and Synthesis",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000154",
    "api_endpoint_template": "/v1/metrics/BEMO:2000154/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000154_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
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    "source_record_hash": "d0050ec2d0692a0a792ec941fce4c076cf8613142effd9ef06a03cab99fa82fe",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 161; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "obo_subset": "bemo_evidence_synthesis_and_certainty",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000155",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000155",
    "preferred_label": "Evidence Sufficiency",
    "normalized_label": "evidence_sufficiency",
    "abbreviation": "",
    "pillar_id": "BEMO:1000001",
    "pillar_label": "Evidence Synthesis and Certainty",
    "category_id": "BEMO:1100006",
    "category_label": "Evidence Certainty and Synthesis",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100006",
    "ontology_namespace": "BEMO",
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    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of evidence sufficiency.",
    "what_it_measures": "Assesses evidence sufficiency using evidence appropriate to evidence certainty and synthesis, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in evidence sufficiency can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "related_frameworks_source": "GRADE; PRISMA; AMSTAR 2; RoB",
    "closely_related_metrics_source": "Evidence Consensus Strength; Evidence Completeness; Evidence Coverage",
    "common_misinterpretations": "Treating evidence sufficiency as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "domain_applicability": "Evidence Certainty and Synthesis",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000155",
    "api_endpoint_template": "/v1/metrics/BEMO:2000155/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000155_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 162,
    "source_record_hash": "516f7f59fc37d19455d99f12f79cf9f0baf5cd671807c3364f013a016d7ec68a",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 162; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "obo_subset": "bemo_evidence_synthesis_and_certainty",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000156",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000156",
    "preferred_label": "Evidence Triangulation Strength",
    "normalized_label": "evidence_triangulation_strength",
    "abbreviation": "",
    "pillar_id": "BEMO:1000001",
    "pillar_label": "Evidence Synthesis and Certainty",
    "category_id": "BEMO:1100006",
    "category_label": "Evidence Certainty and Synthesis",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100006",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting evidence triangulation.",
    "what_it_measures": "Assesses evidence triangulation strength using evidence appropriate to evidence certainty and synthesis, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in evidence triangulation strength can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "related_frameworks_source": "GRADE; PRISMA; AMSTAR 2; RoB",
    "closely_related_metrics_source": "Evidence Robustness; Counterevidence Strength; Missing Evidence Risk",
    "common_misinterpretations": "Treating evidence triangulation strength as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "domain_applicability": "Evidence Certainty and Synthesis",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000156",
    "api_endpoint_template": "/v1/metrics/BEMO:2000156/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000156_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 163,
    "source_record_hash": "b9d887ba211f3aea4699afd087a0aa12fb8ca924209ee34ccda2bfd968c02a4a",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 163; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "obo_subset": "bemo_evidence_synthesis_and_certainty",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000157",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000157",
    "preferred_label": "Information Size Adequacy",
    "normalized_label": "information_size_adequacy",
    "abbreviation": "",
    "pillar_id": "BEMO:1000001",
    "pillar_label": "Evidence Synthesis and Certainty",
    "category_id": "BEMO:1100006",
    "category_label": "Evidence Certainty and Synthesis",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100006",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which information size is sufficient and fit for the stated biomedical inference.",
    "what_it_measures": "Assesses information size adequacy using evidence appropriate to evidence certainty and synthesis, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in information size adequacy can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "related_frameworks_source": "GRADE; PRISMA; AMSTAR 2; RoB",
    "closely_related_metrics_source": "Cumulative Evidence Stability; Multiplicity-Adjusted Credibility",
    "common_misinterpretations": "Treating information size adequacy as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "domain_applicability": "Evidence Certainty and Synthesis",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000157",
    "api_endpoint_template": "/v1/metrics/BEMO:2000157/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000157_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 164,
    "source_record_hash": "1349313eaf86ad90454f8dbf26aa9cb5389132fc9ac2e44b703024851df5136c",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 164; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "obo_subset": "bemo_evidence_synthesis_and_certainty",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000158",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000158",
    "preferred_label": "Missing Evidence Risk",
    "normalized_label": "missing_evidence_risk",
    "abbreviation": "",
    "pillar_id": "BEMO:1000001",
    "pillar_label": "Evidence Synthesis and Certainty",
    "category_id": "BEMO:1100006",
    "category_label": "Evidence Certainty and Synthesis",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100006",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that missing evidence introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses missing evidence risk using evidence appropriate to evidence certainty and synthesis, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in missing evidence risk can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "related_frameworks_source": "GRADE; PRISMA; AMSTAR 2; RoB",
    "closely_related_metrics_source": "Counterevidence Strength; Publication Bias Risk; Selective Nonreporting Risk",
    "common_misinterpretations": "Treating missing evidence risk as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "domain_applicability": "Evidence Certainty and Synthesis",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000158",
    "api_endpoint_template": "/v1/metrics/BEMO:2000158/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000158_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 165,
    "source_record_hash": "ffec67315125f9639a3601d51e352906c34b1c9847a274942f934888c1188977",
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    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 165; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "obo_subset": "bemo_evidence_synthesis_and_certainty",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000159",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000159",
    "preferred_label": "Multiplicity-Adjusted Credibility",
    "normalized_label": "multiplicity_adjusted_credibility",
    "abbreviation": "",
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    "pillar_label": "Evidence Synthesis and Certainty",
    "category_id": "BEMO:1100006",
    "category_label": "Evidence Certainty and Synthesis",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100006",
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    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of multiplicity-adjusted credibility.",
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    "why_it_matters": "Material weakness in multiplicity-adjusted credibility can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "related_frameworks_source": "GRADE; PRISMA; AMSTAR 2; RoB",
    "closely_related_metrics_source": "Information Size Adequacy",
    "common_misinterpretations": "Treating multiplicity-adjusted credibility as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
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    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
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    "study_type_applicability": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "domain_applicability": "Evidence Certainty and Synthesis",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
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    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
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    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 166; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "obo_subset": "bemo_evidence_synthesis_and_certainty",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
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    "metric_id": "BEMO:2000160",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000160",
    "preferred_label": "Overall Evidence Certainty",
    "normalized_label": "overall_evidence_certainty",
    "abbreviation": "",
    "pillar_id": "BEMO:1000001",
    "pillar_label": "Evidence Synthesis and Certainty",
    "category_id": "BEMO:1100006",
    "category_label": "Evidence Certainty and Synthesis",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100006",
    "ontology_namespace": "BEMO",
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    "metric_version": "1.0.0",
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    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of overall evidence certainty.",
    "what_it_measures": "Assesses overall evidence certainty using evidence appropriate to evidence certainty and synthesis, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in overall evidence certainty can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "related_frameworks_source": "GRADE; PRISMA; AMSTAR 2; RoB",
    "closely_related_metrics_source": "Evidence Quality; Evidence Strength",
    "common_misinterpretations": "Treating overall evidence certainty as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
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    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
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    "maximum_value": null,
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    "directionality": "ContextDependentDirection",
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    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
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    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
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    "reviewer": "Unassigned",
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    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
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    "exact_synonyms": "",
    "broad_synonyms": "",
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    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
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    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
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  {
    "metric_id": "BEMO:2000161",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000161",
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    "category_label": "Evidence Certainty and Synthesis",
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    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which prediction interval is sufficient and fit for the stated biomedical inference.",
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    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
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    "applicable_study_types_source": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
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    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
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    "output_datatype": "xsd:string_or_decimal",
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    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
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    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
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    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000161",
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    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 168; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "obo_subset": "bemo_evidence_synthesis_and_certainty",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000162",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000162",
    "preferred_label": "Publication Bias Risk",
    "normalized_label": "publication_bias_risk",
    "abbreviation": "",
    "pillar_id": "BEMO:1000001",
    "pillar_label": "Evidence Synthesis and Certainty",
    "category_id": "BEMO:1100006",
    "category_label": "Evidence Certainty and Synthesis",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100006",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that publication bias introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses publication bias risk using evidence appropriate to evidence certainty and synthesis, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in publication bias risk can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Forest plots; heterogeneity statistics; tau-squared; prediction intervals; funnel plots; regression or selection models; sensitivity analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "related_frameworks_source": "GRADE; PRISMA; AMSTAR 2; RoB",
    "closely_related_metrics_source": "Missing Evidence Risk; Selective Nonreporting Risk; Small-Study Effects",
    "common_misinterpretations": "Treating publication bias risk as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "domain_applicability": "Evidence Certainty and Synthesis",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000162",
    "api_endpoint_template": "/v1/metrics/BEMO:2000162/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000162_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 169,
    "source_record_hash": "ae14a6a3126f2ecd31144006a017263d5e10df0fcde0e6bd8cc0872e93853a7a",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 169; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "obo_subset": "bemo_evidence_synthesis_and_certainty",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000163",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000163",
    "preferred_label": "Selective Nonreporting Risk",
    "normalized_label": "selective_nonreporting_risk",
    "abbreviation": "",
    "pillar_id": "BEMO:1000001",
    "pillar_label": "Evidence Synthesis and Certainty",
    "category_id": "BEMO:1100006",
    "category_label": "Evidence Certainty and Synthesis",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100006",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that selective nonreporting introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses selective nonreporting risk using evidence appropriate to evidence certainty and synthesis, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in selective nonreporting risk can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "related_frameworks_source": "GRADE; PRISMA; AMSTAR 2; RoB",
    "closely_related_metrics_source": "Publication Bias Risk; Small-Study Effects; Study Heterogeneity",
    "common_misinterpretations": "Treating selective nonreporting risk as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "domain_applicability": "Evidence Certainty and Synthesis",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000163",
    "api_endpoint_template": "/v1/metrics/BEMO:2000163/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000163_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 170,
    "source_record_hash": "8c42609174eeba28064b2f75bd158a40f97b17f9cdaa32aed81219eddf87ef89",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 170; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "obo_subset": "bemo_evidence_synthesis_and_certainty",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000164",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000164",
    "preferred_label": "Small-Study Effects",
    "normalized_label": "small_study_effects",
    "abbreviation": "",
    "pillar_id": "BEMO:1000001",
    "pillar_label": "Evidence Synthesis and Certainty",
    "category_id": "BEMO:1100006",
    "category_label": "Evidence Certainty and Synthesis",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100006",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of small-study effects.",
    "what_it_measures": "Assesses small-study effects using evidence appropriate to evidence certainty and synthesis, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in small-study effects can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Forest plots; heterogeneity statistics; tau-squared; prediction intervals; funnel plots; regression or selection models; sensitivity analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "related_frameworks_source": "GRADE; PRISMA; AMSTAR 2; RoB",
    "closely_related_metrics_source": "Selective Nonreporting Risk; Study Heterogeneity; Between-Study Variance",
    "common_misinterpretations": "Treating small-study effects as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "domain_applicability": "Evidence Certainty and Synthesis",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000164",
    "api_endpoint_template": "/v1/metrics/BEMO:2000164/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000164_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 171,
    "source_record_hash": "ec5ee159f748d5035209ae456b71092c6724bc73af9b720bf70afe3ffc41f242",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 171; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "obo_subset": "bemo_evidence_synthesis_and_certainty",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000165",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000165",
    "preferred_label": "Study Heterogeneity",
    "normalized_label": "study_heterogeneity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000001",
    "pillar_label": "Evidence Synthesis and Certainty",
    "category_id": "BEMO:1100006",
    "category_label": "Evidence Certainty and Synthesis",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100006",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of study heterogeneity.",
    "what_it_measures": "Assesses study heterogeneity using evidence appropriate to evidence certainty and synthesis, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in study heterogeneity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Forest plots; heterogeneity statistics; tau-squared; prediction intervals; funnel plots; regression or selection models; sensitivity analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "related_frameworks_source": "GRADE; PRISMA; AMSTAR 2; RoB",
    "closely_related_metrics_source": "Small-Study Effects; Between-Study Variance; Prediction Interval Adequacy",
    "common_misinterpretations": "Treating study heterogeneity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Systematic reviews, meta-analyses, evidence profiles, guidelines",
    "domain_applicability": "Evidence Certainty and Synthesis",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000165",
    "api_endpoint_template": "/v1/metrics/BEMO:2000165/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000165_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 172,
    "source_record_hash": "93fce0e52f596e9f5e6b6636a82da697803846e686e6144faa894115a270196a",
    "source_references": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 172; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/",
    "obo_subset": "bemo_evidence_synthesis_and_certainty",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000166",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000166",
    "preferred_label": "Age Appropriateness",
    "normalized_label": "age_appropriateness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100007",
    "category_label": "Experimental Biology and Animal Research",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100007",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which age is sufficient and fit for the stated biomedical inference.",
    "what_it_measures": "Assesses age appropriateness using evidence appropriate to experimental biology and animal research, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in age appropriateness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "related_frameworks_source": "ARRIVE 2.0; SYRCLE; OECD",
    "closely_related_metrics_source": "Sex as a Biological Variable Adequacy; Genetic Background Control; Housing and Husbandry Control",
    "common_misinterpretations": "Treating age appropriateness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "domain_applicability": "Experimental Biology and Animal Research",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000166",
    "api_endpoint_template": "/v1/metrics/BEMO:2000166/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000166_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 173,
    "source_record_hash": "6f50922de3489bf44a56c621fcc8933973821a524b4c3ba13cb746276b4a9bea",
    "source_references": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 173; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000167",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000167",
    "preferred_label": "Animal Model Construct Validity",
    "normalized_label": "animal_model_construct_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100007",
    "category_label": "Experimental Biology and Animal Research",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100007",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which animal model construct supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses animal model construct validity using evidence appropriate to experimental biology and animal research, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in animal model construct validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "related_frameworks_source": "ARRIVE 2.0; SYRCLE; OECD",
    "closely_related_metrics_source": "Animal Model Face Validity; Animal Model Predictive Validity; Species Appropriateness",
    "common_misinterpretations": "Treating animal model construct validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "domain_applicability": "Experimental Biology and Animal Research",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000167",
    "api_endpoint_template": "/v1/metrics/BEMO:2000167/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000167_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 174,
    "source_record_hash": "f8c928bcc279a4856d6377104c402fb4a00d102300c3c3fa14181f174b53f974",
    "source_references": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 174; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000168",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000168",
    "preferred_label": "Animal Model Face Validity",
    "normalized_label": "animal_model_face_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100007",
    "category_label": "Experimental Biology and Animal Research",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100007",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which animal model face supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses animal model face validity using evidence appropriate to experimental biology and animal research, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in animal model face validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "related_frameworks_source": "ARRIVE 2.0; SYRCLE; OECD",
    "closely_related_metrics_source": "Blinding in Experimental Assessment; Animal Model Construct Validity; Animal Model Predictive Validity",
    "common_misinterpretations": "Treating animal model face validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "domain_applicability": "Experimental Biology and Animal Research",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000168",
    "api_endpoint_template": "/v1/metrics/BEMO:2000168/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000168_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 175,
    "source_record_hash": "1bc9d94635678f728d2a96fd7016f3d61e24c78d9e33c5093213c9d715511534",
    "source_references": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 175; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000169",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000169",
    "preferred_label": "Animal Model Predictive Validity",
    "normalized_label": "animal_model_predictive_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100007",
    "category_label": "Experimental Biology and Animal Research",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100007",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which animal model predictive supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses animal model predictive validity using evidence appropriate to experimental biology and animal research, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in animal model predictive validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "related_frameworks_source": "ARRIVE 2.0; SYRCLE; OECD",
    "closely_related_metrics_source": "Animal Model Construct Validity; Species Appropriateness; Sex as a Biological Variable Adequacy",
    "common_misinterpretations": "Treating animal model predictive validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "domain_applicability": "Experimental Biology and Animal Research",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000169",
    "api_endpoint_template": "/v1/metrics/BEMO:2000169/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000169_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 176,
    "source_record_hash": "ae7f68af5b958c01b88066cf76664c77d333abaff4414b63760b817bf19359d0",
    "source_references": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 176; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000170",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000170",
    "preferred_label": "Attrition Accounting in Animal Studies",
    "normalized_label": "attrition_accounting_in_animal_studies",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100007",
    "category_label": "Experimental Biology and Animal Research",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100007",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of attrition accounting in animal studies.",
    "what_it_measures": "Assesses attrition accounting in animal studies using evidence appropriate to experimental biology and animal research, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in attrition accounting in animal studies can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "related_frameworks_source": "ARRIVE 2.0; SYRCLE; OECD",
    "closely_related_metrics_source": "Humane Endpoint Appropriateness; Exclusion-Criteria Prespecification; Experimental Batch Randomization",
    "common_misinterpretations": "Treating attrition accounting in animal studies as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "domain_applicability": "Experimental Biology and Animal Research",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000170",
    "api_endpoint_template": "/v1/metrics/BEMO:2000170/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000170_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 177,
    "source_record_hash": "bfb6735bf1e0494f94802ec087edc274ccdaea50558f3ea043f6f21ae9210505",
    "source_references": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 177; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000171",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000171",
    "preferred_label": "Biological Replicate Adequacy",
    "normalized_label": "biological_replicate_adequacy",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100007",
    "category_label": "Experimental Biology and Animal Research",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100007",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which biological replicate is sufficient and fit for the stated biomedical inference.",
    "what_it_measures": "Assesses biological replicate adequacy using evidence appropriate to experimental biology and animal research, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in biological replicate adequacy can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "related_frameworks_source": "ARRIVE 2.0; SYRCLE; OECD",
    "closely_related_metrics_source": "Experimental Unit Validity; Technical Replicate Adequacy; Sample Size Justification",
    "common_misinterpretations": "Treating biological replicate adequacy as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "domain_applicability": "Experimental Biology and Animal Research",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000171",
    "api_endpoint_template": "/v1/metrics/BEMO:2000171/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000171_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 178,
    "source_record_hash": "74976e4cf57f53c444f4721c04fc26fb7298cad4ac743db45feeb9a0be34587a",
    "source_references": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 178; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000172",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000172",
    "preferred_label": "Blinding in Experimental Assessment",
    "normalized_label": "blinding_in_experimental_assessment",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100007",
    "category_label": "Experimental Biology and Animal Research",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100007",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of blinding in experimental assessment.",
    "what_it_measures": "Assesses blinding in experimental assessment using evidence appropriate to experimental biology and animal research, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in blinding in experimental assessment can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "related_frameworks_source": "ARRIVE 2.0; SYRCLE; OECD",
    "closely_related_metrics_source": "Randomization in Experimental Allocation; Animal Model Face Validity; Animal Model Construct Validity",
    "common_misinterpretations": "Treating blinding in experimental assessment as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "domain_applicability": "Experimental Biology and Animal Research",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000172",
    "api_endpoint_template": "/v1/metrics/BEMO:2000172/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000172_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 179,
    "source_record_hash": "2a7451a420224db55e7f75f4a33818fc20cbc59d2bbc81f21fd652f7ea1a7931",
    "source_references": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 179; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000173",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000173",
    "preferred_label": "Environmental Standardization",
    "normalized_label": "environmental_standardization",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100007",
    "category_label": "Experimental Biology and Animal Research",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100007",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of environmental standardization.",
    "what_it_measures": "Assesses environmental standardization using evidence appropriate to experimental biology and animal research, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in environmental standardization can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "related_frameworks_source": "ARRIVE 2.0; SYRCLE; OECD",
    "closely_related_metrics_source": "Housing and Husbandry Control; Intervention Fidelity in Animal Studies; Humane Endpoint Appropriateness",
    "common_misinterpretations": "Treating environmental standardization as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "domain_applicability": "Experimental Biology and Animal Research",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000173",
    "api_endpoint_template": "/v1/metrics/BEMO:2000173/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000173_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 180,
    "source_record_hash": "432e96e9d5c02fcda1a353b0ddb2e18d1019ff594f33c248eedfbe337bf31fae",
    "source_references": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 180; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000174",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000174",
    "preferred_label": "Exclusion-Criteria Prespecification",
    "normalized_label": "exclusion_criteria_prespecification",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100007",
    "category_label": "Experimental Biology and Animal Research",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100007",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of exclusion-criteria prespecification.",
    "what_it_measures": "Assesses exclusion-criteria prespecification using evidence appropriate to experimental biology and animal research, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in exclusion-criteria prespecification can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "related_frameworks_source": "ARRIVE 2.0; SYRCLE; OECD",
    "closely_related_metrics_source": "Attrition Accounting in Animal Studies; Experimental Batch Randomization; Positive-Control Performance",
    "common_misinterpretations": "Treating exclusion-criteria prespecification as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "domain_applicability": "Experimental Biology and Animal Research",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000174",
    "api_endpoint_template": "/v1/metrics/BEMO:2000174/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000174_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 181,
    "source_record_hash": "9718ea523adf00e3cd776b8e22423abc28cf080bd659786c7568ddd524ab9208",
    "source_references": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 181; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000175",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000175",
    "preferred_label": "Experimental Batch Randomization",
    "normalized_label": "experimental_batch_randomization",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100007",
    "category_label": "Experimental Biology and Animal Research",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100007",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of experimental batch randomization.",
    "what_it_measures": "Assesses experimental batch randomization using evidence appropriate to experimental biology and animal research, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in experimental batch randomization can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "related_frameworks_source": "ARRIVE 2.0; SYRCLE; OECD",
    "closely_related_metrics_source": "Exclusion-Criteria Prespecification; Positive-Control Performance; Negative-Control Performance",
    "common_misinterpretations": "Treating experimental batch randomization as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "domain_applicability": "Experimental Biology and Animal Research",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000175",
    "api_endpoint_template": "/v1/metrics/BEMO:2000175/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000175_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 182,
    "source_record_hash": "1291027c6f53e5902a86a2cf22b3cca02564dbc940590bb8b8bcfd5004b998b7",
    "source_references": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 182; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000176",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000176",
    "preferred_label": "Experimental Unit Validity",
    "normalized_label": "experimental_unit_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100007",
    "category_label": "Experimental Biology and Animal Research",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100007",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which experimental unit supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses experimental unit validity using evidence appropriate to experimental biology and animal research, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in experimental unit validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "related_frameworks_source": "ARRIVE 2.0; SYRCLE; OECD",
    "closely_related_metrics_source": "Biological Replicate Adequacy; Technical Replicate Adequacy",
    "common_misinterpretations": "Treating experimental unit validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "domain_applicability": "Experimental Biology and Animal Research",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000176",
    "api_endpoint_template": "/v1/metrics/BEMO:2000176/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000176_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 183,
    "source_record_hash": "3d08eaaab51eb4d1095b9fb5e884110ba36de86e61615acc1661c581f985a6b1",
    "source_references": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 183; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000177",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000177",
    "preferred_label": "Genetic Background Control",
    "normalized_label": "genetic_background_control",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100007",
    "category_label": "Experimental Biology and Animal Research",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100007",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of genetic background control.",
    "what_it_measures": "Assesses genetic background control using evidence appropriate to experimental biology and animal research, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in genetic background control can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "related_frameworks_source": "ARRIVE 2.0; SYRCLE; OECD",
    "closely_related_metrics_source": "Age Appropriateness; Housing and Husbandry Control; Environmental Standardization",
    "common_misinterpretations": "Treating genetic background control as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "domain_applicability": "Experimental Biology and Animal Research",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000177",
    "api_endpoint_template": "/v1/metrics/BEMO:2000177/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000177_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 184,
    "source_record_hash": "3f6791503c2895971802b5fb5573311999fc32cde51839dc771c56e4855ceb83",
    "source_references": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 184; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000178",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000178",
    "preferred_label": "Housing and Husbandry Control",
    "normalized_label": "housing_and_husbandry_control",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100007",
    "category_label": "Experimental Biology and Animal Research",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100007",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of housing and husbandry control.",
    "what_it_measures": "Assesses housing and husbandry control using evidence appropriate to experimental biology and animal research, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in housing and husbandry control can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "related_frameworks_source": "ARRIVE 2.0; SYRCLE; OECD",
    "closely_related_metrics_source": "Genetic Background Control; Environmental Standardization; Intervention Fidelity in Animal Studies",
    "common_misinterpretations": "Treating housing and husbandry control as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "domain_applicability": "Experimental Biology and Animal Research",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000178",
    "api_endpoint_template": "/v1/metrics/BEMO:2000178/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000178_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 185,
    "source_record_hash": "d4c26e56573de7f55de0caafd1e2880580fe66b8b4d599787ebf0b2bb3808344",
    "source_references": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 185; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000179",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000179",
    "preferred_label": "Humane Endpoint Appropriateness",
    "normalized_label": "humane_endpoint_appropriateness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100007",
    "category_label": "Experimental Biology and Animal Research",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100007",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which humane endpoint is sufficient and fit for the stated biomedical inference.",
    "what_it_measures": "Assesses humane endpoint appropriateness using evidence appropriate to experimental biology and animal research, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in humane endpoint appropriateness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "related_frameworks_source": "ARRIVE 2.0; SYRCLE; OECD",
    "closely_related_metrics_source": "Intervention Fidelity in Animal Studies; Attrition Accounting in Animal Studies; Exclusion-Criteria Prespecification",
    "common_misinterpretations": "Treating humane endpoint appropriateness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "domain_applicability": "Experimental Biology and Animal Research",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000179",
    "api_endpoint_template": "/v1/metrics/BEMO:2000179/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000179_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 186,
    "source_record_hash": "efafe26c06dac15c0d485bfb264933c40fe9cf7ca97c5195ea92c9cfeb3f7a98",
    "source_references": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 186; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000180",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000180",
    "preferred_label": "Intervention Fidelity in Animal Studies",
    "normalized_label": "intervention_fidelity_in_animal_studies",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100007",
    "category_label": "Experimental Biology and Animal Research",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100007",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of intervention fidelity in animal studies.",
    "what_it_measures": "Assesses intervention fidelity in animal studies using evidence appropriate to experimental biology and animal research, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in intervention fidelity in animal studies can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "related_frameworks_source": "ARRIVE 2.0; SYRCLE; OECD",
    "closely_related_metrics_source": "Environmental Standardization; Humane Endpoint Appropriateness; Attrition Accounting in Animal Studies",
    "common_misinterpretations": "Treating intervention fidelity in animal studies as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "domain_applicability": "Experimental Biology and Animal Research",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000180",
    "api_endpoint_template": "/v1/metrics/BEMO:2000180/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000180_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 187,
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    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 187; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
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    "xrefs": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
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    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
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    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
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  {
    "metric_id": "BEMO:2000181",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000181",
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    "normalized_label": "negative_control_performance",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
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    "category_label": "Experimental Biology and Animal Research",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100007",
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    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of negative-control performance.",
    "what_it_measures": "Assesses negative-control performance using evidence appropriate to experimental biology and animal research, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in negative-control performance can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "related_frameworks_source": "ARRIVE 2.0; SYRCLE; OECD",
    "closely_related_metrics_source": "Positive-Control Performance; Vehicle-Control Validity; Orthogonal Validation",
    "common_misinterpretations": "Treating negative-control performance as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "domain_applicability": "Experimental Biology and Animal Research",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
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    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000181_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
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    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 188; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
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    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
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    "metric_id": "BEMO:2000182",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000182",
    "preferred_label": "Orthogonal Validation",
    "normalized_label": "orthogonal_validation",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100007",
    "category_label": "Experimental Biology and Animal Research",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100007",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of orthogonal validation.",
    "what_it_measures": "Assesses orthogonal validation using evidence appropriate to experimental biology and animal research, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in orthogonal validation can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "related_frameworks_source": "ARRIVE 2.0; SYRCLE; OECD",
    "closely_related_metrics_source": "Vehicle-Control Validity; Technical Artifact Exclusion",
    "common_misinterpretations": "Treating orthogonal validation as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
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    "study_type_applicability": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "domain_applicability": "Experimental Biology and Animal Research",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
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    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
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    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
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    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
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    "metric_id": "BEMO:2000183",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000183",
    "preferred_label": "Positive-Control Performance",
    "normalized_label": "positive_control_performance",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
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    "category_label": "Experimental Biology and Animal Research",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100007",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
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    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of positive-control performance.",
    "what_it_measures": "Assesses positive-control performance using evidence appropriate to experimental biology and animal research, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in positive-control performance can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "related_frameworks_source": "ARRIVE 2.0; SYRCLE; OECD",
    "closely_related_metrics_source": "Experimental Batch Randomization; Negative-Control Performance; Vehicle-Control Validity",
    "common_misinterpretations": "Treating positive-control performance as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
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    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
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    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
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    "study_type_applicability": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "domain_applicability": "Experimental Biology and Animal Research",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
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    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000183_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
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    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 190; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000184",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000184",
    "preferred_label": "Randomization in Experimental Allocation",
    "normalized_label": "randomization_in_experimental_allocation",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100007",
    "category_label": "Experimental Biology and Animal Research",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100007",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of randomization in experimental allocation.",
    "what_it_measures": "Assesses randomization in experimental allocation using evidence appropriate to experimental biology and animal research, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in randomization in experimental allocation can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "related_frameworks_source": "ARRIVE 2.0; SYRCLE; OECD",
    "closely_related_metrics_source": "Sample Size Justification; Blinding in Experimental Assessment; Animal Model Face Validity",
    "common_misinterpretations": "Treating randomization in experimental allocation as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "domain_applicability": "Experimental Biology and Animal Research",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000184",
    "api_endpoint_template": "/v1/metrics/BEMO:2000184/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000184_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 191,
    "source_record_hash": "5cc94b6085b9c596d4f74c18712e9f8177db4335ab703b2218b9c3a63209c113",
    "source_references": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 191; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000185",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000185",
    "preferred_label": "Sample Size Justification",
    "normalized_label": "sample_size_justification",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100007",
    "category_label": "Experimental Biology and Animal Research",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100007",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of sample size justification.",
    "what_it_measures": "Assesses sample size justification using evidence appropriate to experimental biology and animal research, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in sample size justification can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "related_frameworks_source": "ARRIVE 2.0; SYRCLE; OECD",
    "closely_related_metrics_source": "Technical Replicate Adequacy; Randomization in Experimental Allocation; Blinding in Experimental Assessment",
    "common_misinterpretations": "Treating sample size justification as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "domain_applicability": "Experimental Biology and Animal Research",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000185",
    "api_endpoint_template": "/v1/metrics/BEMO:2000185/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000185_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 192,
    "source_record_hash": "9c4289123cb7c0f9d87fa9453151e360a9b6781cd9fbb6f6b26a09f4543b0dab",
    "source_references": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 192; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000186",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000186",
    "preferred_label": "Sex as a Biological Variable Adequacy",
    "normalized_label": "sex_as_a_biological_variable_adequacy",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100007",
    "category_label": "Experimental Biology and Animal Research",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100007",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which sex as a biological variable is sufficient and fit for the stated biomedical inference.",
    "what_it_measures": "Assesses sex as a biological variable adequacy using evidence appropriate to experimental biology and animal research, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in sex as a biological variable adequacy can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "related_frameworks_source": "ARRIVE 2.0; SYRCLE; OECD",
    "closely_related_metrics_source": "Species Appropriateness; Age Appropriateness; Genetic Background Control",
    "common_misinterpretations": "Treating sex as a biological variable adequacy as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "domain_applicability": "Experimental Biology and Animal Research",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000186",
    "api_endpoint_template": "/v1/metrics/BEMO:2000186/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000186_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 193,
    "source_record_hash": "67d1bc84f2c2d0324ee734ed3d2df1c72cd4820b21290b5a8b136d75863a4866",
    "source_references": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 193; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000187",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000187",
    "preferred_label": "Species Appropriateness",
    "normalized_label": "species_appropriateness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100007",
    "category_label": "Experimental Biology and Animal Research",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100007",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which species is sufficient and fit for the stated biomedical inference.",
    "what_it_measures": "Assesses species appropriateness using evidence appropriate to experimental biology and animal research, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in species appropriateness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "related_frameworks_source": "ARRIVE 2.0; SYRCLE; OECD",
    "closely_related_metrics_source": "Animal Model Predictive Validity; Sex as a Biological Variable Adequacy; Age Appropriateness",
    "common_misinterpretations": "Treating species appropriateness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "domain_applicability": "Experimental Biology and Animal Research",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000187",
    "api_endpoint_template": "/v1/metrics/BEMO:2000187/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000187_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 194,
    "source_record_hash": "93f7de14ca784e8a47e3c6ab351c1e75c21a4c3e26305cfe63e0d4fef2122575",
    "source_references": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 194; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000188",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000188",
    "preferred_label": "Technical Artifact Exclusion",
    "normalized_label": "technical_artifact_exclusion",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100007",
    "category_label": "Experimental Biology and Animal Research",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100007",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of technical artifact exclusion.",
    "what_it_measures": "Assesses technical artifact exclusion using evidence appropriate to experimental biology and animal research, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in technical artifact exclusion can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "related_frameworks_source": "ARRIVE 2.0; SYRCLE; OECD",
    "closely_related_metrics_source": "Orthogonal Validation",
    "common_misinterpretations": "Treating technical artifact exclusion as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "domain_applicability": "Experimental Biology and Animal Research",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000188",
    "api_endpoint_template": "/v1/metrics/BEMO:2000188/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000188_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 195,
    "source_record_hash": "8d21017136fa388d87b531d9b552fc3f6787a0b2615866e0c0a1ca9ae2fb0bbf",
    "source_references": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 195; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000189",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000189",
    "preferred_label": "Technical Replicate Adequacy",
    "normalized_label": "technical_replicate_adequacy",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100007",
    "category_label": "Experimental Biology and Animal Research",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100007",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which technical replicate is sufficient and fit for the stated biomedical inference.",
    "what_it_measures": "Assesses technical replicate adequacy using evidence appropriate to experimental biology and animal research, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in technical replicate adequacy can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "related_frameworks_source": "ARRIVE 2.0; SYRCLE; OECD",
    "closely_related_metrics_source": "Biological Replicate Adequacy; Sample Size Justification; Randomization in Experimental Allocation",
    "common_misinterpretations": "Treating technical replicate adequacy as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "domain_applicability": "Experimental Biology and Animal Research",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000189",
    "api_endpoint_template": "/v1/metrics/BEMO:2000189/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000189_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 196,
    "source_record_hash": "8f5bd5eed372632eafdff28f1c8035067d4634c207012fb089ff55a67d705176",
    "source_references": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 196; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000190",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000190",
    "preferred_label": "Vehicle-Control Validity",
    "normalized_label": "vehicle_control_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000006",
    "pillar_label": "Biological Mechanism and Experimental Evidence",
    "category_id": "BEMO:1100007",
    "category_label": "Experimental Biology and Animal Research",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100007",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which vehicle-control supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses vehicle-control validity using evidence appropriate to experimental biology and animal research, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in vehicle-control validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "related_frameworks_source": "ARRIVE 2.0; SYRCLE; OECD",
    "closely_related_metrics_source": "Negative-Control Performance; Orthogonal Validation; Technical Artifact Exclusion",
    "common_misinterpretations": "Treating vehicle-control validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "In vitro, ex vivo, organoid, animal, and preclinical experiments",
    "domain_applicability": "Experimental Biology and Animal Research",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000190",
    "api_endpoint_template": "/v1/metrics/BEMO:2000190/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000190_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 197,
    "source_record_hash": "b1aee501d417f186bec79f011141586c66408c5b9c272dd6db3a4fa3a34f419d",
    "source_references": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 197; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://arriveguidelines.org/arrive-guidelines | https://www.radboudumc.nl/en/research/departments/health-evidence/systematic-review-center-for-laboratory-animal-experimentation | https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm",
    "obo_subset": "bemo_biological_mechanism_and_experimental_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000191",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000191",
    "preferred_label": "Care-Pathway Independence",
    "normalized_label": "care_pathway_independence",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100008",
    "category_label": "External Validity and Applicability",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100008",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of care-pathway independence.",
    "what_it_measures": "Assesses care-pathway independence using evidence appropriate to external validity and applicability, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in care-pathway independence can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "related_frameworks_source": "GRADE; QUADAS-2; CONSORT; STROBE",
    "closely_related_metrics_source": "Disease-Severity Generalizability; Context Sensitivity; Ecological Validity",
    "common_misinterpretations": "Treating care-pathway independence as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "domain_applicability": "External Validity and Applicability",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000191",
    "api_endpoint_template": "/v1/metrics/BEMO:2000191/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000191_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 198,
    "source_record_hash": "e39c9004563f895f591d754f0c2c01d5cfe45a0e26d44584ecb91c07d72c494a",
    "source_references": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 198; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000192",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000192",
    "preferred_label": "Comparator Applicability",
    "normalized_label": "comparator_applicability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100008",
    "category_label": "External Validity and Applicability",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100008",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of comparator applicability.",
    "what_it_measures": "Assesses comparator applicability using evidence appropriate to external validity and applicability, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in comparator applicability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "related_frameworks_source": "GRADE; QUADAS-2; CONSORT; STROBE",
    "closely_related_metrics_source": "Intervention Applicability; Outcome Applicability; Spectrum Representativeness",
    "common_misinterpretations": "Treating comparator applicability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "domain_applicability": "External Validity and Applicability",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000192",
    "api_endpoint_template": "/v1/metrics/BEMO:2000192/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000192_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 199,
    "source_record_hash": "607cceee390b7cb8ce577becf5db87c7c9a4643da6c8fbe5bd44948e1b9e3853",
    "source_references": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 199; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000193",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000193",
    "preferred_label": "Context Sensitivity",
    "normalized_label": "context_sensitivity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100008",
    "category_label": "External Validity and Applicability",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100008",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of context sensitivity.",
    "what_it_measures": "Assesses context sensitivity using evidence appropriate to external validity and applicability, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in context sensitivity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified threshold; valid reference standard; complete 2×2 classification; confidence intervals; spectrum and prevalence assessment.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "related_frameworks_source": "GRADE; QUADAS-2; CONSORT; STROBE",
    "closely_related_metrics_source": "Care-Pathway Independence; Ecological Validity; Real-World Evidence Alignment",
    "common_misinterpretations": "Treating context sensitivity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "domain_applicability": "External Validity and Applicability",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000193",
    "api_endpoint_template": "/v1/metrics/BEMO:2000193/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000193_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 200,
    "source_record_hash": "84e49bfba34c254503c96b181528bf2beab33e58bfa3d6d711b6afaa740ea566",
    "source_references": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 200; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000194",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000194",
    "preferred_label": "Demographic Generalizability",
    "normalized_label": "demographic_generalizability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100008",
    "category_label": "External Validity and Applicability",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100008",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of demographic generalizability.",
    "what_it_measures": "Assesses demographic generalizability using evidence appropriate to external validity and applicability, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in demographic generalizability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "related_frameworks_source": "GRADE; QUADAS-2; CONSORT; STROBE",
    "closely_related_metrics_source": "Temporal Generalizability; Disease-Severity Generalizability; Care-Pathway Independence",
    "common_misinterpretations": "Treating demographic generalizability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "domain_applicability": "External Validity and Applicability",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000194",
    "api_endpoint_template": "/v1/metrics/BEMO:2000194/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000194_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 201,
    "source_record_hash": "e22341c32d6f7aad19740ed4b08e7f5ffc168107f1e04a79ba4ec60f6b92c463",
    "source_references": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 201; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000195",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000195",
    "preferred_label": "Disease-Severity Generalizability",
    "normalized_label": "disease_severity_generalizability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100008",
    "category_label": "External Validity and Applicability",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100008",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of disease-severity generalizability.",
    "what_it_measures": "Assesses disease-severity generalizability using evidence appropriate to external validity and applicability, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in disease-severity generalizability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "related_frameworks_source": "GRADE; QUADAS-2; CONSORT; STROBE",
    "closely_related_metrics_source": "Demographic Generalizability; Care-Pathway Independence; Context Sensitivity",
    "common_misinterpretations": "Treating disease-severity generalizability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "domain_applicability": "External Validity and Applicability",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000195",
    "api_endpoint_template": "/v1/metrics/BEMO:2000195/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000195_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 202,
    "source_record_hash": "867ff07055e7596b98039def11c9ce9ca056af7a3a11134bb8f46a0bd5adc97a",
    "source_references": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 202; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000196",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000196",
    "preferred_label": "Ecological Validity",
    "normalized_label": "ecological_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100008",
    "category_label": "External Validity and Applicability",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100008",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which ecological supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses ecological validity using evidence appropriate to external validity and applicability, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in ecological validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "related_frameworks_source": "GRADE; QUADAS-2; CONSORT; STROBE",
    "closely_related_metrics_source": "Context Sensitivity; Real-World Evidence Alignment",
    "common_misinterpretations": "Treating ecological validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "domain_applicability": "External Validity and Applicability",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000196",
    "api_endpoint_template": "/v1/metrics/BEMO:2000196/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000196_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 203,
    "source_record_hash": "04e73707dc619457f6718e0be03029ef6e99208f68cbcad30d9f5bb20b2cd94b",
    "source_references": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 203; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000197",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000197",
    "preferred_label": "External Validity",
    "normalized_label": "external_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100008",
    "category_label": "External Validity and Applicability",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100008",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which external supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses external validity using evidence appropriate to external validity and applicability, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in external validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "related_frameworks_source": "GRADE; QUADAS-2; CONSORT; STROBE",
    "closely_related_metrics_source": "Population Representativeness; Sampling Frame Adequacy",
    "common_misinterpretations": "Treating external validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "domain_applicability": "External Validity and Applicability",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000197",
    "api_endpoint_template": "/v1/metrics/BEMO:2000197/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000197_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 204,
    "source_record_hash": "291600cbcf719af0c4e82629e00cccabf1b55b19eff672c1fb6c5c7fe2ec4338",
    "source_references": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 204; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000198",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000198",
    "preferred_label": "Generalizability",
    "normalized_label": "generalizability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100008",
    "category_label": "External Validity and Applicability",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100008",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of generalizability.",
    "what_it_measures": "Assesses generalizability using evidence appropriate to external validity and applicability, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in generalizability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "related_frameworks_source": "GRADE; QUADAS-2; CONSORT; STROBE",
    "closely_related_metrics_source": "Transportability; Setting Applicability; Population Applicability",
    "common_misinterpretations": "Treating generalizability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "domain_applicability": "External Validity and Applicability",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000198",
    "api_endpoint_template": "/v1/metrics/BEMO:2000198/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000198_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 205,
    "source_record_hash": "27f8a61447192cbdeaaa7e84078183a3604b2e6ac6c0df13be6cfe9e4a09224a",
    "source_references": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 205; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000199",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000199",
    "preferred_label": "Geographic Consistency",
    "normalized_label": "geographic_consistency",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100008",
    "category_label": "External Validity and Applicability",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100008",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree of agreement in geographic across measurements, studies, methods, populations, or biological levels.",
    "what_it_measures": "Assesses geographic consistency using evidence appropriate to external validity and applicability, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in geographic consistency can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "related_frameworks_source": "GRADE; QUADAS-2; CONSORT; STROBE",
    "closely_related_metrics_source": "Subgroup Consistency; Temporal Generalizability; Demographic Generalizability",
    "common_misinterpretations": "Treating geographic consistency as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "domain_applicability": "External Validity and Applicability",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000199",
    "api_endpoint_template": "/v1/metrics/BEMO:2000199/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000199_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 206,
    "source_record_hash": "22cb03e816656f6f9ad7a2acb4c32a01ffbc6b40d04a48011cef0a52134d504e",
    "source_references": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 206; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000200",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000200",
    "preferred_label": "Intervention Applicability",
    "normalized_label": "intervention_applicability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100008",
    "category_label": "External Validity and Applicability",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100008",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of intervention applicability.",
    "what_it_measures": "Assesses intervention applicability using evidence appropriate to external validity and applicability, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in intervention applicability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "related_frameworks_source": "GRADE; QUADAS-2; CONSORT; STROBE",
    "closely_related_metrics_source": "Population Applicability; Comparator Applicability; Outcome Applicability",
    "common_misinterpretations": "Treating intervention applicability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "domain_applicability": "External Validity and Applicability",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000200",
    "api_endpoint_template": "/v1/metrics/BEMO:2000200/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000200_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 207,
    "source_record_hash": "d1cb3929ecc9b0976fba4823cb5a09ca13a634dd6efaa3ee43969eafe3250a95",
    "source_references": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 207; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000201",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000201",
    "preferred_label": "Outcome Applicability",
    "normalized_label": "outcome_applicability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100008",
    "category_label": "External Validity and Applicability",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100008",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of outcome applicability.",
    "what_it_measures": "Assesses outcome applicability using evidence appropriate to external validity and applicability, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in outcome applicability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "related_frameworks_source": "GRADE; QUADAS-2; CONSORT; STROBE",
    "closely_related_metrics_source": "Comparator Applicability; Spectrum Representativeness; Subgroup Consistency",
    "common_misinterpretations": "Treating outcome applicability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "domain_applicability": "External Validity and Applicability",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000201",
    "api_endpoint_template": "/v1/metrics/BEMO:2000201/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000201_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 208,
    "source_record_hash": "5c0db0a0257f7b171655d97624fdf4764d1fabad77716300abc92c2debe71f7d",
    "source_references": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 208; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000202",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000202",
    "preferred_label": "Population Applicability",
    "normalized_label": "population_applicability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100008",
    "category_label": "External Validity and Applicability",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100008",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of population applicability.",
    "what_it_measures": "Assesses population applicability using evidence appropriate to external validity and applicability, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in population applicability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "related_frameworks_source": "GRADE; QUADAS-2; CONSORT; STROBE",
    "closely_related_metrics_source": "Setting Applicability; Intervention Applicability; Comparator Applicability",
    "common_misinterpretations": "Treating population applicability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "domain_applicability": "External Validity and Applicability",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000202",
    "api_endpoint_template": "/v1/metrics/BEMO:2000202/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000202_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 209,
    "source_record_hash": "9073b7f8b73fc788aa084d5c4ac174d69482c2a1439b22f86a39e465503328bc",
    "source_references": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 209; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000203",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000203",
    "preferred_label": "Population Representativeness",
    "normalized_label": "population_representativeness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100008",
    "category_label": "External Validity and Applicability",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100008",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of population representativeness.",
    "what_it_measures": "Assesses population representativeness using evidence appropriate to external validity and applicability, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in population representativeness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "related_frameworks_source": "GRADE; QUADAS-2; CONSORT; STROBE",
    "closely_related_metrics_source": "External Validity; Sampling Frame Adequacy; Transportability",
    "common_misinterpretations": "Treating population representativeness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "domain_applicability": "External Validity and Applicability",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000203",
    "api_endpoint_template": "/v1/metrics/BEMO:2000203/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000203_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 210,
    "source_record_hash": "efa730876069251ed2dde336a59f381b8c109c4ee429da0b68bf8bae61b0ba48",
    "source_references": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 210; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000204",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000204",
    "preferred_label": "Real-World Evidence Alignment",
    "normalized_label": "real_world_evidence_alignment",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100008",
    "category_label": "External Validity and Applicability",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100008",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of real-world evidence alignment.",
    "what_it_measures": "Assesses real-world evidence alignment using evidence appropriate to external validity and applicability, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in real-world evidence alignment can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "related_frameworks_source": "GRADE; QUADAS-2; CONSORT; STROBE",
    "closely_related_metrics_source": "Ecological Validity",
    "common_misinterpretations": "Treating real-world evidence alignment as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "domain_applicability": "External Validity and Applicability",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000204",
    "api_endpoint_template": "/v1/metrics/BEMO:2000204/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000204_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 211,
    "source_record_hash": "2bcc973aa3f12efded260e2aef1541636262ee110856a34255ce0823d91dfb20",
    "source_references": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 211; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000205",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000205",
    "preferred_label": "Sampling Frame Adequacy",
    "normalized_label": "sampling_frame_adequacy",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100008",
    "category_label": "External Validity and Applicability",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100008",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which sampling frame is sufficient and fit for the stated biomedical inference.",
    "what_it_measures": "Assesses sampling frame adequacy using evidence appropriate to external validity and applicability, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in sampling frame adequacy can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "related_frameworks_source": "GRADE; QUADAS-2; CONSORT; STROBE",
    "closely_related_metrics_source": "Population Representativeness; Transportability; Generalizability",
    "common_misinterpretations": "Treating sampling frame adequacy as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "domain_applicability": "External Validity and Applicability",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000205",
    "api_endpoint_template": "/v1/metrics/BEMO:2000205/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000205_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 212,
    "source_record_hash": "39b818e971de479787fde11a4523a1b0d31f5dcbc88f645b968cff60fa6bf381",
    "source_references": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 212; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000206",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000206",
    "preferred_label": "Setting Applicability",
    "normalized_label": "setting_applicability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100008",
    "category_label": "External Validity and Applicability",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100008",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of setting applicability.",
    "what_it_measures": "Assesses setting applicability using evidence appropriate to external validity and applicability, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in setting applicability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "related_frameworks_source": "GRADE; QUADAS-2; CONSORT; STROBE",
    "closely_related_metrics_source": "Generalizability; Population Applicability; Intervention Applicability",
    "common_misinterpretations": "Treating setting applicability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "domain_applicability": "External Validity and Applicability",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000206",
    "api_endpoint_template": "/v1/metrics/BEMO:2000206/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000206_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 213,
    "source_record_hash": "323f595d53815c626b380456c55c73f7ff5e2e10beb1e0ffc44edb8067c37e86",
    "source_references": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 213; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000207",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000207",
    "preferred_label": "Spectrum Representativeness",
    "normalized_label": "spectrum_representativeness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100008",
    "category_label": "External Validity and Applicability",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100008",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of spectrum representativeness.",
    "what_it_measures": "Assesses spectrum representativeness using evidence appropriate to external validity and applicability, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in spectrum representativeness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Target-decoy analysis; spectral scoring; reference standards; replicate injections; retention-time and mass-error monitoring; orthogonal confirmation.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "related_frameworks_source": "GRADE; QUADAS-2; CONSORT; STROBE",
    "closely_related_metrics_source": "Outcome Applicability; Subgroup Consistency; Geographic Consistency",
    "common_misinterpretations": "Treating spectrum representativeness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "domain_applicability": "External Validity and Applicability",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000207",
    "api_endpoint_template": "/v1/metrics/BEMO:2000207/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000207_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 214,
    "source_record_hash": "771c727a328004aa438f83d20410cd3600ce67ac5affa57fc6e9aaee55cb7ed9",
    "source_references": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 214; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000208",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000208",
    "preferred_label": "Subgroup Consistency",
    "normalized_label": "subgroup_consistency",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100008",
    "category_label": "External Validity and Applicability",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100008",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree of agreement in subgroup across measurements, studies, methods, populations, or biological levels.",
    "what_it_measures": "Assesses subgroup consistency using evidence appropriate to external validity and applicability, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in subgroup consistency can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "related_frameworks_source": "GRADE; QUADAS-2; CONSORT; STROBE",
    "closely_related_metrics_source": "Spectrum Representativeness; Geographic Consistency; Temporal Generalizability",
    "common_misinterpretations": "Treating subgroup consistency as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "domain_applicability": "External Validity and Applicability",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000208",
    "api_endpoint_template": "/v1/metrics/BEMO:2000208/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000208_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 215,
    "source_record_hash": "26cabc1a909ce4ef7d5d54dc609f85f9fea3829985a8f8573b3da07a3e225f5b",
    "source_references": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 215; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000209",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000209",
    "preferred_label": "Temporal Generalizability",
    "normalized_label": "temporal_generalizability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100008",
    "category_label": "External Validity and Applicability",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100008",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of temporal generalizability.",
    "what_it_measures": "Assesses temporal generalizability using evidence appropriate to external validity and applicability, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in temporal generalizability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "related_frameworks_source": "GRADE; QUADAS-2; CONSORT; STROBE",
    "closely_related_metrics_source": "Geographic Consistency; Demographic Generalizability; Disease-Severity Generalizability",
    "common_misinterpretations": "Treating temporal generalizability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "domain_applicability": "External Validity and Applicability",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000209",
    "api_endpoint_template": "/v1/metrics/BEMO:2000209/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000209_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 216,
    "source_record_hash": "dc35bc0fc74498ddd3acc1a47faf52ec96fba459b80f9800025d1a3d1e674317",
    "source_references": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 216; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000210",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000210",
    "preferred_label": "Transportability",
    "normalized_label": "transportability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000005",
    "pillar_label": "External Validity, Biomarkers, and Clinical Evidence",
    "category_id": "BEMO:1100008",
    "category_label": "External Validity and Applicability",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100008",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of transportability.",
    "what_it_measures": "Assesses transportability using evidence appropriate to external validity and applicability, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in transportability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Body of evidence / synthesis / outcome",
    "applicable_study_types_source": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "related_frameworks_source": "GRADE; QUADAS-2; CONSORT; STROBE",
    "closely_related_metrics_source": "Sampling Frame Adequacy; Generalizability; Setting Applicability",
    "common_misinterpretations": "Treating transportability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Body of evidence / synthesis / outcome",
    "study_type_applicability": "Clinical, epidemiologic, diagnostic, translational, and population studies",
    "domain_applicability": "External Validity and Applicability",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000210",
    "api_endpoint_template": "/v1/metrics/BEMO:2000210/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000210_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 217,
    "source_record_hash": "ef0b46b07942a1780f9e2e890b09b7edc3579f016762848aa46c4d956da3075d",
    "source_references": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 217; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/",
    "obo_subset": "bemo_external_validity_biomarkers_and_clinical_evidence",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000211",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000211",
    "preferred_label": "Allelic Evidence Strength",
    "normalized_label": "allelic_evidence_strength",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100009",
    "category_label": "Genetics and Variant Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100009",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting allelic evidence.",
    "what_it_measures": "Assesses allelic evidence strength using evidence appropriate to genetics and variant evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in allelic evidence strength can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "ClinGen/ACMG evidence scoring; pedigree analysis; population databases; case-control data; functional assays; expert-panel review.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "related_frameworks_source": "ClinGen; ACMG AMP; STREGA; Gene Ontology",
    "closely_related_metrics_source": "De Novo Evidence Strength; Case-Level Evidence Strength; Case-Control Evidence Strength",
    "common_misinterpretations": "Treating allelic evidence strength as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "domain_applicability": "Genetics and Variant Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000211",
    "api_endpoint_template": "/v1/metrics/BEMO:2000211/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000211_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 218,
    "source_record_hash": "2dd4a685750034c6175101f0128d889784cf621fed0cf93a74098e6b4879332b",
    "source_references": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 218; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000212",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000212",
    "preferred_label": "Case-Control Evidence Strength",
    "normalized_label": "case_control_evidence_strength",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100009",
    "category_label": "Genetics and Variant Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100009",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting case-control evidence.",
    "what_it_measures": "Assesses case-control evidence strength using evidence appropriate to genetics and variant evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in case-control evidence strength can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "related_frameworks_source": "ClinGen; ACMG AMP; STREGA; Gene Ontology",
    "closely_related_metrics_source": "Case-Level Evidence Strength; Functional Variant Evidence; Computational Variant Evidence",
    "common_misinterpretations": "Treating case-control evidence strength as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "domain_applicability": "Genetics and Variant Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000212",
    "api_endpoint_template": "/v1/metrics/BEMO:2000212/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000212_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 219,
    "source_record_hash": "a2868c878aff5e68e6f9aeb87fd5a98fd776f1ca106d2e9dbad34a8cc81ecfd8",
    "source_references": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 219; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000213",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000213",
    "preferred_label": "Case-Level Evidence Strength",
    "normalized_label": "case_level_evidence_strength",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100009",
    "category_label": "Genetics and Variant Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100009",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting case-level evidence.",
    "what_it_measures": "Assesses case-level evidence strength using evidence appropriate to genetics and variant evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in case-level evidence strength can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "related_frameworks_source": "ClinGen; ACMG AMP; STREGA; Gene Ontology",
    "closely_related_metrics_source": "Allelic Evidence Strength; Case-Control Evidence Strength; Functional Variant Evidence",
    "common_misinterpretations": "Treating case-level evidence strength as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "domain_applicability": "Genetics and Variant Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000213",
    "api_endpoint_template": "/v1/metrics/BEMO:2000213/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000213_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 220,
    "source_record_hash": "e9e681d8a3c5b4ca82348a6cd8fe70f3f48bd8351d482c3aa492a6712873c3db",
    "source_references": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 220; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000214",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000214",
    "preferred_label": "Co-segregation Likelihood",
    "normalized_label": "co_segregation_likelihood",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100009",
    "category_label": "Genetics and Variant Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100009",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of co-segregation likelihood.",
    "what_it_measures": "Assesses co-segregation likelihood using evidence appropriate to genetics and variant evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in co-segregation likelihood can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "ClinGen/ACMG evidence scoring; pedigree analysis; population databases; case-control data; functional assays; expert-panel review.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "related_frameworks_source": "ClinGen; ACMG AMP; STREGA; Gene Ontology",
    "closely_related_metrics_source": "RNA Evidence Strength; Penetrance Evidence; Expressivity Consistency",
    "common_misinterpretations": "Treating co-segregation likelihood as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "domain_applicability": "Genetics and Variant Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000214",
    "api_endpoint_template": "/v1/metrics/BEMO:2000214/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000214_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 221,
    "source_record_hash": "965b0273f9a305e64b50437dcad85ab39818fad51d561d0ac4da1daaf7d204f2",
    "source_references": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 221; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000215",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000215",
    "preferred_label": "Computational Variant Evidence",
    "normalized_label": "computational_variant_evidence",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100009",
    "category_label": "Genetics and Variant Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100009",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of computational variant evidence.",
    "what_it_measures": "Assesses computational variant evidence using evidence appropriate to genetics and variant evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in computational variant evidence can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "ClinGen/ACMG evidence scoring; pedigree analysis; population databases; case-control data; functional assays; expert-panel review.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "related_frameworks_source": "ClinGen; ACMG AMP; STREGA; Gene Ontology",
    "closely_related_metrics_source": "Functional Variant Evidence; Phenotypic Specificity for Variant; Variant Phase Evidence",
    "common_misinterpretations": "Treating computational variant evidence as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "domain_applicability": "Genetics and Variant Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000215",
    "api_endpoint_template": "/v1/metrics/BEMO:2000215/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000215_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 222,
    "source_record_hash": "1f84faa3d8c87f3b1ed44b62077d2c489782ab72b149d6009c127395a0070a10",
    "source_references": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 222; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000216",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000216",
    "preferred_label": "Conflicting Interpretation Burden",
    "normalized_label": "conflicting_interpretation_burden",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100009",
    "category_label": "Genetics and Variant Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100009",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of conflicting interpretation burden.",
    "what_it_measures": "Assesses conflicting interpretation burden using evidence appropriate to genetics and variant evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in conflicting interpretation burden can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "related_frameworks_source": "ClinGen; ACMG AMP; STREGA; Gene Ontology",
    "closely_related_metrics_source": "Variant Classification Stability",
    "common_misinterpretations": "Treating conflicting interpretation burden as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "domain_applicability": "Genetics and Variant Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000216",
    "api_endpoint_template": "/v1/metrics/BEMO:2000216/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000216_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 223,
    "source_record_hash": "54567aec6ae0bbdadfae015005c07328ab45d161c0cc6d36f9e5198150b2b29e",
    "source_references": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 223; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000217",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000217",
    "preferred_label": "De Novo Evidence Strength",
    "normalized_label": "de_novo_evidence_strength",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100009",
    "category_label": "Genetics and Variant Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100009",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting de novo evidence.",
    "what_it_measures": "Assesses de novo evidence strength using evidence appropriate to genetics and variant evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in de novo evidence strength can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "ClinGen/ACMG evidence scoring; pedigree analysis; population databases; case-control data; functional assays; expert-panel review.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "related_frameworks_source": "ClinGen; ACMG AMP; STREGA; Gene Ontology",
    "closely_related_metrics_source": "Segregation Evidence Strength; Allelic Evidence Strength; Case-Level Evidence Strength",
    "common_misinterpretations": "Treating de novo evidence strength as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "domain_applicability": "Genetics and Variant Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000217",
    "api_endpoint_template": "/v1/metrics/BEMO:2000217/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000217_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 224,
    "source_record_hash": "e1a17a41d450c91691b405a890d0fa9af7ecd8fed12385f8124d85b912c16860",
    "source_references": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 224; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000218",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000218",
    "preferred_label": "Expressivity Consistency",
    "normalized_label": "expressivity_consistency",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100009",
    "category_label": "Genetics and Variant Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100009",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree of agreement in expressivity across measurements, studies, methods, populations, or biological levels.",
    "what_it_measures": "Assesses expressivity consistency using evidence appropriate to genetics and variant evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in expressivity consistency can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "related_frameworks_source": "ClinGen; ACMG AMP; STREGA; Gene Ontology",
    "closely_related_metrics_source": "Penetrance Evidence; Founder-Effect Assessment; Phenocopy Risk",
    "common_misinterpretations": "Treating expressivity consistency as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "domain_applicability": "Genetics and Variant Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000218",
    "api_endpoint_template": "/v1/metrics/BEMO:2000218/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000218_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 225,
    "source_record_hash": "d100842d4d2c367ecd1122df00784975aa0a773a92bbb5c68a8ff23fbbd4dfc4",
    "source_references": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 225; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000219",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000219",
    "preferred_label": "Founder-Effect Assessment",
    "normalized_label": "founder_effect_assessment",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100009",
    "category_label": "Genetics and Variant Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100009",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of founder-effect assessment.",
    "what_it_measures": "Assesses founder-effect assessment using evidence appropriate to genetics and variant evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in founder-effect assessment can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "related_frameworks_source": "ClinGen; ACMG AMP; STREGA; Gene Ontology",
    "closely_related_metrics_source": "Expressivity Consistency; Phenocopy Risk; Locus Heterogeneity Assessment",
    "common_misinterpretations": "Treating founder-effect assessment as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "domain_applicability": "Genetics and Variant Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000219",
    "api_endpoint_template": "/v1/metrics/BEMO:2000219/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000219_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 226,
    "source_record_hash": "6530e53b02059e4bfd6465ae64ac385198a560d8a80df4ba701894a8c5cb0975",
    "source_references": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 226; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000220",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000220",
    "preferred_label": "Functional Variant Evidence",
    "normalized_label": "functional_variant_evidence",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100009",
    "category_label": "Genetics and Variant Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100009",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of functional variant evidence.",
    "what_it_measures": "Assesses functional variant evidence using evidence appropriate to genetics and variant evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in functional variant evidence can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "ClinGen/ACMG evidence scoring; pedigree analysis; population databases; case-control data; functional assays; expert-panel review.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "related_frameworks_source": "ClinGen; ACMG AMP; STREGA; Gene Ontology",
    "closely_related_metrics_source": "Case-Control Evidence Strength; Computational Variant Evidence; Phenotypic Specificity for Variant",
    "common_misinterpretations": "Treating functional variant evidence as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "domain_applicability": "Genetics and Variant Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000220",
    "api_endpoint_template": "/v1/metrics/BEMO:2000220/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000220_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 227,
    "source_record_hash": "7a71bec12dfb580d6d32593ad450868d51a755f2a8b35e7eee350ad98d24c73e",
    "source_references": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 227; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000221",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000221",
    "preferred_label": "Gene–Disease Validity",
    "normalized_label": "gene_disease_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100009",
    "category_label": "Genetics and Variant Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100009",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which gene–disease supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses gene–disease validity using evidence appropriate to genetics and variant evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in gene–disease validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "ClinGen/ACMG evidence scoring; pedigree analysis; population databases; case-control data; functional assays; expert-panel review.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "related_frameworks_source": "ClinGen; ACMG AMP; STREGA; Gene Ontology",
    "closely_related_metrics_source": "Variant Pathogenicity Evidence Strength; Population Frequency Compatibility",
    "common_misinterpretations": "Treating gene–disease validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "domain_applicability": "Genetics and Variant Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000221",
    "api_endpoint_template": "/v1/metrics/BEMO:2000221/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000221_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 228,
    "source_record_hash": "4501a0d637c0d3d7b3852d3be8f61115b2b1ac442582dd9a3ec88bd21dad9f7c",
    "source_references": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 228; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000222",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000222",
    "preferred_label": "Genotype–Phenotype Concordance",
    "normalized_label": "genotype_phenotype_concordance",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100009",
    "category_label": "Genetics and Variant Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100009",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
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    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree of agreement in genotype–phenotype across measurements, studies, methods, populations, or biological levels.",
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    "why_it_matters": "Material weakness in genotype–phenotype concordance can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Read- and variant-level quality-control summaries; replicate concordance; orthogonal confirmation; benchmarking against reference materials.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "related_frameworks_source": "ClinGen; ACMG AMP; STREGA; Gene Ontology",
    "closely_related_metrics_source": "Locus Heterogeneity Assessment; Variant Classification Stability; Conflicting Interpretation Burden",
    "common_misinterpretations": "Treating genotype–phenotype concordance as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "domain_applicability": "Genetics and Variant Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
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    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000222",
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    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000222_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
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    "source_record_hash": "baeee8e900a9ffef8f3ddd054b3a12f2233d89fc626f852fd31efc4b84b81685",
    "source_references": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 229; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000223",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000223",
    "preferred_label": "Hotspot/Functional-Domain Evidence",
    "normalized_label": "hotspot_functional_domain_evidence",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100009",
    "category_label": "Genetics and Variant Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100009",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of hotspot/functional-domain evidence.",
    "what_it_measures": "Assesses hotspot/functional-domain evidence using evidence appropriate to genetics and variant evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in hotspot/functional-domain evidence can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "related_frameworks_source": "ClinGen; ACMG AMP; STREGA; Gene Ontology",
    "closely_related_metrics_source": "Loss-of-Function Mechanism Validity; Null-Variant Quality; Splicing Evidence Strength",
    "common_misinterpretations": "Treating hotspot/functional-domain evidence as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "domain_applicability": "Genetics and Variant Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000223",
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    "provenance_model": "W3C PROV-O",
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    "source_sheet": "Biomedical Evidence Metrics",
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    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 230; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
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  {
    "metric_id": "BEMO:2000224",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000224",
    "preferred_label": "Locus Heterogeneity Assessment",
    "normalized_label": "locus_heterogeneity_assessment",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100009",
    "category_label": "Genetics and Variant Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100009",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of locus heterogeneity assessment.",
    "what_it_measures": "Assesses locus heterogeneity assessment using evidence appropriate to genetics and variant evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in locus heterogeneity assessment can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Forest plots; heterogeneity statistics; tau-squared; prediction intervals; funnel plots; regression or selection models; sensitivity analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "related_frameworks_source": "ClinGen; ACMG AMP; STREGA; Gene Ontology",
    "closely_related_metrics_source": "Phenocopy Risk; Genotype–Phenotype Concordance; Variant Classification Stability",
    "common_misinterpretations": "Treating locus heterogeneity assessment as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "domain_applicability": "Genetics and Variant Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000224",
    "api_endpoint_template": "/v1/metrics/BEMO:2000224/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000224_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 231,
    "source_record_hash": "bd3af304ec15826df5f67db7f079c0ba66a1f5f5a3e852d600550186267f50cb",
    "source_references": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 231; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000225",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000225",
    "preferred_label": "Loss-of-Function Mechanism Validity",
    "normalized_label": "loss_of_function_mechanism_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100009",
    "category_label": "Genetics and Variant Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100009",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which loss-of-function mechanism supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses loss-of-function mechanism validity using evidence appropriate to genetics and variant evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in loss-of-function mechanism validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "related_frameworks_source": "ClinGen; ACMG AMP; STREGA; Gene Ontology",
    "closely_related_metrics_source": "Variant Phase Evidence; Hotspot/Functional-Domain Evidence; Null-Variant Quality",
    "common_misinterpretations": "Treating loss-of-function mechanism validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "domain_applicability": "Genetics and Variant Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000225",
    "api_endpoint_template": "/v1/metrics/BEMO:2000225/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000225_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 232,
    "source_record_hash": "a389d5411c414282451fe5495bf2c1c444f06ae12cd17457edf93df2953dc32e",
    "source_references": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 232; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000226",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000226",
    "preferred_label": "Null-Variant Quality",
    "normalized_label": "null_variant_quality",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100009",
    "category_label": "Genetics and Variant Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100009",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of null-variant quality.",
    "what_it_measures": "Assesses null-variant quality using evidence appropriate to genetics and variant evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in null-variant quality can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "ClinGen/ACMG evidence scoring; pedigree analysis; population databases; case-control data; functional assays; expert-panel review.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "related_frameworks_source": "ClinGen; ACMG AMP; STREGA; Gene Ontology",
    "closely_related_metrics_source": "Hotspot/Functional-Domain Evidence; Splicing Evidence Strength; RNA Evidence Strength",
    "common_misinterpretations": "Treating null-variant quality as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "domain_applicability": "Genetics and Variant Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000226",
    "api_endpoint_template": "/v1/metrics/BEMO:2000226/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000226_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 233,
    "source_record_hash": "de2f4749e64a7014070a28c9c8587efaf4dbb9b3583c2ab6e78cd6826c00de34",
    "source_references": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 233; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000227",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000227",
    "preferred_label": "Penetrance Evidence",
    "normalized_label": "penetrance_evidence",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100009",
    "category_label": "Genetics and Variant Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100009",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of penetrance evidence.",
    "what_it_measures": "Assesses penetrance evidence using evidence appropriate to genetics and variant evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in penetrance evidence can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "ClinGen/ACMG evidence scoring; pedigree analysis; population databases; case-control data; functional assays; expert-panel review.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "related_frameworks_source": "ClinGen; ACMG AMP; STREGA; Gene Ontology",
    "closely_related_metrics_source": "Co-segregation Likelihood; Expressivity Consistency; Founder-Effect Assessment",
    "common_misinterpretations": "Treating penetrance evidence as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "domain_applicability": "Genetics and Variant Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000227",
    "api_endpoint_template": "/v1/metrics/BEMO:2000227/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000227_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 234,
    "source_record_hash": "83c8ddff797d0831554af5cae66094d559ff9fcf3cefc498edc05f2c18b6ee97",
    "source_references": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 234; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000228",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000228",
    "preferred_label": "Phenocopy Risk",
    "normalized_label": "phenocopy_risk",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100009",
    "category_label": "Genetics and Variant Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100009",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that phenocopy introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses phenocopy risk using evidence appropriate to genetics and variant evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in phenocopy risk can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "related_frameworks_source": "ClinGen; ACMG AMP; STREGA; Gene Ontology",
    "closely_related_metrics_source": "Founder-Effect Assessment; Locus Heterogeneity Assessment; Genotype–Phenotype Concordance",
    "common_misinterpretations": "Treating phenocopy risk as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "domain_applicability": "Genetics and Variant Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000228",
    "api_endpoint_template": "/v1/metrics/BEMO:2000228/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000228_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 235,
    "source_record_hash": "eba377fe2c190b6390cd804f64874ad58540debe287184cfa259e70d97d1fcc8",
    "source_references": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 235; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000229",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000229",
    "preferred_label": "Phenotypic Specificity for Variant",
    "normalized_label": "phenotypic_specificity_for_variant",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100009",
    "category_label": "Genetics and Variant Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100009",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of phenotypic specificity for variant.",
    "what_it_measures": "Assesses phenotypic specificity for variant using evidence appropriate to genetics and variant evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in phenotypic specificity for variant can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified threshold; valid reference standard; complete 2×2 classification; confidence intervals; spectrum and prevalence assessment.",
    "methods_of_assessment": "ClinGen/ACMG evidence scoring; pedigree analysis; population databases; case-control data; functional assays; expert-panel review.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "related_frameworks_source": "ClinGen; ACMG AMP; STREGA; Gene Ontology",
    "closely_related_metrics_source": "Computational Variant Evidence; Variant Phase Evidence; Loss-of-Function Mechanism Validity",
    "common_misinterpretations": "Treating phenotypic specificity for variant as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "domain_applicability": "Genetics and Variant Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000229",
    "api_endpoint_template": "/v1/metrics/BEMO:2000229/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000229_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 236,
    "source_record_hash": "ae0b81578c2487ac58cc25c0925e5e5b5580990b17b1391fc512e266a26a2788",
    "source_references": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 236; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000230",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000230",
    "preferred_label": "Population Frequency Compatibility",
    "normalized_label": "population_frequency_compatibility",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100009",
    "category_label": "Genetics and Variant Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100009",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of population frequency compatibility.",
    "what_it_measures": "Assesses population frequency compatibility using evidence appropriate to genetics and variant evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in population frequency compatibility can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "related_frameworks_source": "ClinGen; ACMG AMP; STREGA; Gene Ontology",
    "closely_related_metrics_source": "Variant Pathogenicity Evidence Strength; Segregation Evidence Strength; De Novo Evidence Strength",
    "common_misinterpretations": "Treating population frequency compatibility as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "domain_applicability": "Genetics and Variant Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000230",
    "api_endpoint_template": "/v1/metrics/BEMO:2000230/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000230_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 237,
    "source_record_hash": "da2b6bc79f60e4e8121c9a5cd9a562fbe0d255feef3ecb78f1de13bffe50a0f4",
    "source_references": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 237; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000231",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000231",
    "preferred_label": "RNA Evidence Strength",
    "normalized_label": "rna_evidence_strength",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100009",
    "category_label": "Genetics and Variant Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100009",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting rna evidence.",
    "what_it_measures": "Assesses rna evidence strength using evidence appropriate to genetics and variant evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in rna evidence strength can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "related_frameworks_source": "ClinGen; ACMG AMP; STREGA; Gene Ontology",
    "closely_related_metrics_source": "Splicing Evidence Strength; Co-segregation Likelihood; Penetrance Evidence",
    "common_misinterpretations": "Treating rna evidence strength as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "domain_applicability": "Genetics and Variant Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000231",
    "api_endpoint_template": "/v1/metrics/BEMO:2000231/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000231_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 238,
    "source_record_hash": "8e776a34bb92ed3d093c7eb03481f1c61ce724a0995235355586c28e53418e35",
    "source_references": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 238; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000232",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000232",
    "preferred_label": "Segregation Evidence Strength",
    "normalized_label": "segregation_evidence_strength",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100009",
    "category_label": "Genetics and Variant Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100009",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting segregation evidence.",
    "what_it_measures": "Assesses segregation evidence strength using evidence appropriate to genetics and variant evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in segregation evidence strength can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "ClinGen/ACMG evidence scoring; pedigree analysis; population databases; case-control data; functional assays; expert-panel review.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "related_frameworks_source": "ClinGen; ACMG AMP; STREGA; Gene Ontology",
    "closely_related_metrics_source": "Population Frequency Compatibility; De Novo Evidence Strength; Allelic Evidence Strength",
    "common_misinterpretations": "Treating segregation evidence strength as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "domain_applicability": "Genetics and Variant Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000232",
    "api_endpoint_template": "/v1/metrics/BEMO:2000232/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000232_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 239,
    "source_record_hash": "4f9bdcfda63260ced3f40796d43228eea03ead68f517bc87939698d4f5d4faf2",
    "source_references": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 239; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000233",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000233",
    "preferred_label": "Splicing Evidence Strength",
    "normalized_label": "splicing_evidence_strength",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100009",
    "category_label": "Genetics and Variant Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100009",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting splicing evidence.",
    "what_it_measures": "Assesses splicing evidence strength using evidence appropriate to genetics and variant evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in splicing evidence strength can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "related_frameworks_source": "ClinGen; ACMG AMP; STREGA; Gene Ontology",
    "closely_related_metrics_source": "Null-Variant Quality; RNA Evidence Strength; Co-segregation Likelihood",
    "common_misinterpretations": "Treating splicing evidence strength as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "domain_applicability": "Genetics and Variant Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000233",
    "api_endpoint_template": "/v1/metrics/BEMO:2000233/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000233_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 240,
    "source_record_hash": "50c6384810a1443b5a98f42466fb8ab2489b57dad29ed2dab35ef7acec1960d2",
    "source_references": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 240; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000234",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000234",
    "preferred_label": "Variant Classification Stability",
    "normalized_label": "variant_classification_stability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100009",
    "category_label": "Genetics and Variant Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100009",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of variant classification stability.",
    "what_it_measures": "Assesses variant classification stability using evidence appropriate to genetics and variant evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in variant classification stability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "ClinGen/ACMG evidence scoring; pedigree analysis; population databases; case-control data; functional assays; expert-panel review.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "related_frameworks_source": "ClinGen; ACMG AMP; STREGA; Gene Ontology",
    "closely_related_metrics_source": "Genotype–Phenotype Concordance; Conflicting Interpretation Burden",
    "common_misinterpretations": "Treating variant classification stability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "domain_applicability": "Genetics and Variant Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000234",
    "api_endpoint_template": "/v1/metrics/BEMO:2000234/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000234_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 241,
    "source_record_hash": "103d1dc365ad36d3caee0208333084352e814015d8cdbebbb9964106d3315f21",
    "source_references": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 241; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000235",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000235",
    "preferred_label": "Variant Pathogenicity Evidence Strength",
    "normalized_label": "variant_pathogenicity_evidence_strength",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100009",
    "category_label": "Genetics and Variant Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100009",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting variant pathogenicity evidence.",
    "what_it_measures": "Assesses variant pathogenicity evidence strength using evidence appropriate to genetics and variant evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in variant pathogenicity evidence strength can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "ClinGen/ACMG evidence scoring; pedigree analysis; population databases; case-control data; functional assays; expert-panel review.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "related_frameworks_source": "ClinGen; ACMG AMP; STREGA; Gene Ontology",
    "closely_related_metrics_source": "Gene–Disease Validity; Population Frequency Compatibility; Segregation Evidence Strength",
    "common_misinterpretations": "Treating variant pathogenicity evidence strength as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "domain_applicability": "Genetics and Variant Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000235",
    "api_endpoint_template": "/v1/metrics/BEMO:2000235/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000235_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 242,
    "source_record_hash": "ce239eedae0622eb1018ab2bfc52cd2d32ef0a5f6a874008c2d8838deb99bd4a",
    "source_references": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 242; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000236",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000236",
    "preferred_label": "Variant Phase Evidence",
    "normalized_label": "variant_phase_evidence",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100009",
    "category_label": "Genetics and Variant Evidence",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100009",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of variant phase evidence.",
    "what_it_measures": "Assesses variant phase evidence using evidence appropriate to genetics and variant evidence, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in variant phase evidence can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "ClinGen/ACMG evidence scoring; pedigree analysis; population databases; case-control data; functional assays; expert-panel review.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "related_frameworks_source": "ClinGen; ACMG AMP; STREGA; Gene Ontology",
    "closely_related_metrics_source": "Phenotypic Specificity for Variant; Loss-of-Function Mechanism Validity; Hotspot/Functional-Domain Evidence",
    "common_misinterpretations": "Treating variant phase evidence as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mendelian disease, cancer genetics, association, segregation, and functional studies",
    "domain_applicability": "Genetics and Variant Evidence",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000236",
    "api_endpoint_template": "/v1/metrics/BEMO:2000236/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000236_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 243,
    "source_record_hash": "e63350cbc225389693f86f1ceb6c24e47930b1a6b522574479bcaf1390376503",
    "source_references": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 243; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://clinicalgenome.org/curation-activities/gene-disease-validity/ | https://pubmed.ncbi.nlm.nih.gov/25741868/ | https://www.equator-network.org/reporting-guidelines/strega/ | https://geneontology.org/docs/guide-go-evidence-codes/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000237",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000237",
    "preferred_label": "Allelic Balance",
    "normalized_label": "allelic_balance",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of allelic balance.",
    "what_it_measures": "Assesses allelic balance using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in allelic balance can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "ClinGen/ACMG evidence scoring; pedigree analysis; population databases; case-control data; functional assays; expert-panel review.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Genotype Quality; Strand Bias; Reference Bias",
    "common_misinterpretations": "Treating allelic balance as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000237",
    "api_endpoint_template": "/v1/metrics/BEMO:2000237/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000237_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 244,
    "source_record_hash": "0857b2292263da43e4b892ac8b30335b2a7fd8730d0baae8269f0919f1da549b",
    "source_references": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 244; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000238",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000238",
    "preferred_label": "Alternative Splicing Validation",
    "normalized_label": "alternative_splicing_validation",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of alternative splicing validation.",
    "what_it_measures": "Assesses alternative splicing validation using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in alternative splicing validation can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Transcript Quantification Reliability; Single-Cell Doublet Burden; Single-Cell Ambient RNA Burden",
    "common_misinterpretations": "Treating alternative splicing validation as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000238",
    "api_endpoint_template": "/v1/metrics/BEMO:2000238/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000238_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 245,
    "source_record_hash": "64b27913521868b5a9491d569eb82729fee0c3cb2133bfc9132e110785fa8847",
    "source_references": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 245; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000239",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000239",
    "preferred_label": "Batch-Effect Control",
    "normalized_label": "batch_effect_control",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of batch-effect control.",
    "what_it_measures": "Assesses batch-effect control using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in batch-effect control can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Hardy–Weinberg Equilibrium Compatibility; Population Stratification Control; Relatedness Control",
    "common_misinterpretations": "Treating batch-effect control as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000239",
    "api_endpoint_template": "/v1/metrics/BEMO:2000239/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000239_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 246,
    "source_record_hash": "0751d3491af658db1257b3b04a366a751c7fd0fdfb5e615ebbae3dab6970c7c9",
    "source_references": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 246; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000240",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000240",
    "preferred_label": "Call-Rate Completeness",
    "normalized_label": "call_rate_completeness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which all scientifically necessary components of call-rate are present, documented, and evaluable.",
    "what_it_measures": "Assesses call-rate completeness using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in call-rate completeness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Read- and variant-level quality-control summaries; replicate concordance; orthogonal confirmation; benchmarking against reference materials.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Reference Bias; Hardy–Weinberg Equilibrium Compatibility; Batch-Effect Control",
    "common_misinterpretations": "Treating call-rate completeness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000240",
    "api_endpoint_template": "/v1/metrics/BEMO:2000240/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000240_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 247,
    "source_record_hash": "c69a25da4615faa5675944ca32d4c5ec30a0c44f5216034581329797d9a32abc",
    "source_references": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 247; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000241",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000241",
    "preferred_label": "Cell-Type Annotation Confidence",
    "normalized_label": "cell_type_annotation_confidence",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The justified degree of certainty assigned to cell-type annotation given the quantity, quality, consistency, and limitations of supporting evidence.",
    "what_it_measures": "Assesses cell-type annotation confidence using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in cell-type annotation confidence can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Single-Cell Feature Detection Rate; Spatial Transcriptomic Registration Accuracy; Cross-Platform Genomic Concordance",
    "common_misinterpretations": "Treating cell-type annotation confidence as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000241",
    "api_endpoint_template": "/v1/metrics/BEMO:2000241/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000241_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 248,
    "source_record_hash": "f7aebc612affb172059739df32608fb7c4d69384f1ff8c565432595eea6b9937",
    "source_references": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 248; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000242",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000242",
    "preferred_label": "Contamination Burden",
    "normalized_label": "contamination_burden",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of contamination burden.",
    "what_it_measures": "Assesses contamination burden using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in contamination burden can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Library Complexity; Sample Identity Concordance; Sex Concordance",
    "common_misinterpretations": "Treating contamination burden as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000242",
    "api_endpoint_template": "/v1/metrics/BEMO:2000242/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000242_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 249,
    "source_record_hash": "fc0cd98bc92235d469bf2bc025f0d327d8170dfb4df97b973710a8d887eff3f4",
    "source_references": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 249; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000243",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000243",
    "preferred_label": "Cross-Platform Genomic Concordance",
    "normalized_label": "cross_platform_genomic_concordance",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree of agreement in cross-platform genomic across measurements, studies, methods, populations, or biological levels.",
    "what_it_measures": "Assesses cross-platform genomic concordance using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in cross-platform genomic concordance can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Spatial Transcriptomic Registration Accuracy",
    "common_misinterpretations": "Treating cross-platform genomic concordance as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000243",
    "api_endpoint_template": "/v1/metrics/BEMO:2000243/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000243_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 250,
    "source_record_hash": "91130249c6d3c5254de370a79251a5dce82ecc1afbe7b1276235f59ee93b7b5a",
    "source_references": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 250; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000244",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000244",
    "preferred_label": "Differential Expression Robustness",
    "normalized_label": "differential_expression_robustness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of differential expression robustness.",
    "what_it_measures": "Assesses differential expression robustness using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in differential expression robustness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Relatedness Control; Normalization Adequacy; Transcript Quantification Reliability",
    "common_misinterpretations": "Treating differential expression robustness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000244",
    "api_endpoint_template": "/v1/metrics/BEMO:2000244/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000244_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 251,
    "source_record_hash": "e70802b2991914211c0dcd91213c02319dd673fc93963b9e2064b8bca944c528",
    "source_references": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 251; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000245",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000245",
    "preferred_label": "Duplicate Read Burden",
    "normalized_label": "duplicate_read_burden",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of duplicate read burden.",
    "what_it_measures": "Assesses duplicate read burden using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in duplicate read burden can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Read- and variant-level quality-control summaries; replicate concordance; orthogonal confirmation; benchmarking against reference materials.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Read Quality; Library Complexity; Contamination Burden",
    "common_misinterpretations": "Treating duplicate read burden as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000245",
    "api_endpoint_template": "/v1/metrics/BEMO:2000245/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000245_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 252,
    "source_record_hash": "c1d6b63aea87c65750f96b5e3a771c6866843a2e5ba7e8081dd07af03bc0e9c5",
    "source_references": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 252; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000246",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000246",
    "preferred_label": "Genome Coverage Uniformity",
    "normalized_label": "genome_coverage_uniformity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The proportion and representativeness of the relevant genome uniformity captured by the evidence or measurement process.",
    "what_it_measures": "Assesses genome coverage uniformity using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in genome coverage uniformity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Sequencing Depth Adequacy; Mapping Quality; Read Quality",
    "common_misinterpretations": "Treating genome coverage uniformity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000246",
    "api_endpoint_template": "/v1/metrics/BEMO:2000246/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000246_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 253,
    "source_record_hash": "c86e8ba8cbfb79ea4dbc1a9a4cd5da76837e35c7f45f5966b51b9734760bdf1f",
    "source_references": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 253; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000247",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000247",
    "preferred_label": "Genotype Quality",
    "normalized_label": "genotype_quality",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of genotype quality.",
    "what_it_measures": "Assesses genotype quality using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in genotype quality can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Read- and variant-level quality-control summaries; replicate concordance; orthogonal confirmation; benchmarking against reference materials.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Variant Call Quality; Allelic Balance; Strand Bias",
    "common_misinterpretations": "Treating genotype quality as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000247",
    "api_endpoint_template": "/v1/metrics/BEMO:2000247/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000247_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 254,
    "source_record_hash": "6b3ff41c46f655393bf02a8730b778b41b8fad3c6f62302d7543aef197484ea3",
    "source_references": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 254; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000248",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000248",
    "preferred_label": "Hardy–Weinberg Equilibrium Compatibility",
    "normalized_label": "hardy_weinberg_equilibrium_compatibility",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of hardy–weinberg equilibrium compatibility.",
    "what_it_measures": "Assesses hardy–weinberg equilibrium compatibility using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in hardy–weinberg equilibrium compatibility can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Call-Rate Completeness; Batch-Effect Control; Population Stratification Control",
    "common_misinterpretations": "Treating hardy–weinberg equilibrium compatibility as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000248",
    "api_endpoint_template": "/v1/metrics/BEMO:2000248/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000248_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 255,
    "source_record_hash": "158d6abc0d325612b86f33eeb0aa8e0dbdfd4460dc9c1934f90601f28ed25284",
    "source_references": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 255; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000249",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000249",
    "preferred_label": "Library Complexity",
    "normalized_label": "library_complexity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of library complexity.",
    "what_it_measures": "Assesses library complexity using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in library complexity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Duplicate Read Burden; Contamination Burden; Sample Identity Concordance",
    "common_misinterpretations": "Treating library complexity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000249",
    "api_endpoint_template": "/v1/metrics/BEMO:2000249/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000249_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 256,
    "source_record_hash": "fb650cc4b9fc46d550895b59d1656dada1a7ec625426686e0a708ba75b6fc5f0",
    "source_references": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 256; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000250",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000250",
    "preferred_label": "Mapping Quality",
    "normalized_label": "mapping_quality",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of mapping quality.",
    "what_it_measures": "Assesses mapping quality using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in mapping quality can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Read- and variant-level quality-control summaries; replicate concordance; orthogonal confirmation; benchmarking against reference materials.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Genome Coverage Uniformity; Read Quality; Duplicate Read Burden",
    "common_misinterpretations": "Treating mapping quality as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000250",
    "api_endpoint_template": "/v1/metrics/BEMO:2000250/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000250_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 257,
    "source_record_hash": "aef9eeffa971170a3db3642e806206bdf35806d1d8cc427e16ad9106f7e0207c",
    "source_references": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 257; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000251",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000251",
    "preferred_label": "Normalization Adequacy",
    "normalized_label": "normalization_adequacy",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which normalization is sufficient and fit for the stated biomedical inference.",
    "what_it_measures": "Assesses normalization adequacy using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in normalization adequacy can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Differential Expression Robustness; Transcript Quantification Reliability; Alternative Splicing Validation",
    "common_misinterpretations": "Treating normalization adequacy as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000251",
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    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000251_AssessmentShape",
    "provenance_model": "W3C PROV-O",
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    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 258; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000252",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000252",
    "preferred_label": "Population Stratification Control",
    "normalized_label": "population_stratification_control",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of population stratification control.",
    "what_it_measures": "Assesses population stratification control using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in population stratification control can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Batch-Effect Control; Relatedness Control; Differential Expression Robustness",
    "common_misinterpretations": "Treating population stratification control as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000252",
    "api_endpoint_template": "/v1/metrics/BEMO:2000252/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000252_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 259,
    "source_record_hash": "c82d16c5b00c0127f5b02c510a48d677f57d7580cba4dcb68dce1141e1686c1d",
    "source_references": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 259; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000253",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000253",
    "preferred_label": "Read Quality",
    "normalized_label": "read_quality",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of read quality.",
    "what_it_measures": "Assesses read quality using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in read quality can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Read- and variant-level quality-control summaries; replicate concordance; orthogonal confirmation; benchmarking against reference materials.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Mapping Quality; Duplicate Read Burden; Library Complexity",
    "common_misinterpretations": "Treating read quality as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000253",
    "api_endpoint_template": "/v1/metrics/BEMO:2000253/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000253_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 260,
    "source_record_hash": "e9483af6db486496b6f4b0c18d333bb38a6c500a6b80dd23beefe82c05de4acc",
    "source_references": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 260; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000254",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000254",
    "preferred_label": "Reference Bias",
    "normalized_label": "reference_bias",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of reference bias.",
    "what_it_measures": "Assesses reference bias using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in reference bias can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Strand Bias; Call-Rate Completeness; Hardy–Weinberg Equilibrium Compatibility",
    "common_misinterpretations": "Treating reference bias as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000254",
    "api_endpoint_template": "/v1/metrics/BEMO:2000254/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000254_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 261,
    "source_record_hash": "7f170b7ac0b632bb15937074f6f54297bd1374274ba7dd6a71c308a1270c144b",
    "source_references": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 261; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000255",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000255",
    "preferred_label": "Relatedness Control",
    "normalized_label": "relatedness_control",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of relatedness control.",
    "what_it_measures": "Assesses relatedness control using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in relatedness control can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Population Stratification Control; Differential Expression Robustness; Normalization Adequacy",
    "common_misinterpretations": "Treating relatedness control as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000255",
    "api_endpoint_template": "/v1/metrics/BEMO:2000255/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000255_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 262,
    "source_record_hash": "c66c714b8c2b1fb9da08eabc61ab1b346b5733232f7901baf90ed1206b3491ba",
    "source_references": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 262; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000256",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000256",
    "preferred_label": "Sample Identity Concordance",
    "normalized_label": "sample_identity_concordance",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree of agreement in sample identity across measurements, studies, methods, populations, or biological levels.",
    "what_it_measures": "Assesses sample identity concordance using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in sample identity concordance can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Contamination Burden; Sex Concordance; Variant Call Quality",
    "common_misinterpretations": "Treating sample identity concordance as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000256",
    "api_endpoint_template": "/v1/metrics/BEMO:2000256/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000256_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 263,
    "source_record_hash": "cf22f061ff0a6f0403c89f061c9c86c0fdc0e5186e885958801878829549f2cd",
    "source_references": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 263; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000257",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000257",
    "preferred_label": "Sequencing Depth Adequacy",
    "normalized_label": "sequencing_depth_adequacy",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which sequencing depth is sufficient and fit for the stated biomedical inference.",
    "what_it_measures": "Assesses sequencing depth adequacy using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in sequencing depth adequacy can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Read- and variant-level quality-control summaries; replicate concordance; orthogonal confirmation; benchmarking against reference materials.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Genome Coverage Uniformity; Mapping Quality",
    "common_misinterpretations": "Treating sequencing depth adequacy as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000257",
    "api_endpoint_template": "/v1/metrics/BEMO:2000257/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000257_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 264,
    "source_record_hash": "719d5f0d3157f75114503dd8e8b0e75aa481929ab009d6c25b68024c7b5f71a0",
    "source_references": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 264; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000258",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000258",
    "preferred_label": "Sex Concordance",
    "normalized_label": "sex_concordance",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree of agreement in sex across measurements, studies, methods, populations, or biological levels.",
    "what_it_measures": "Assesses sex concordance using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in sex concordance can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Sample Identity Concordance; Variant Call Quality; Genotype Quality",
    "common_misinterpretations": "Treating sex concordance as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000258",
    "api_endpoint_template": "/v1/metrics/BEMO:2000258/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000258_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 265,
    "source_record_hash": "897b2797d8e6449a88906be71f955c7726607e3b28833aef8661c12a890476a4",
    "source_references": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 265; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000259",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000259",
    "preferred_label": "Single-Cell Ambient RNA Burden",
    "normalized_label": "single_cell_ambient_rna_burden",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of single-cell ambient rna burden.",
    "what_it_measures": "Assesses single-cell ambient rna burden using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in single-cell ambient rna burden can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Single-Cell Doublet Burden; Single-Cell Viability; Single-Cell Feature Detection Rate",
    "common_misinterpretations": "Treating single-cell ambient rna burden as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000259",
    "api_endpoint_template": "/v1/metrics/BEMO:2000259/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000259_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 266,
    "source_record_hash": "1685a23504d9a42b00cb2ea9bdca0c2daeec5f3be11cc0d479a9acb5349c658a",
    "source_references": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 266; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000260",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000260",
    "preferred_label": "Single-Cell Doublet Burden",
    "normalized_label": "single_cell_doublet_burden",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of single-cell doublet burden.",
    "what_it_measures": "Assesses single-cell doublet burden using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in single-cell doublet burden can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Alternative Splicing Validation; Single-Cell Ambient RNA Burden; Single-Cell Viability",
    "common_misinterpretations": "Treating single-cell doublet burden as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000260",
    "api_endpoint_template": "/v1/metrics/BEMO:2000260/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000260_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 267,
    "source_record_hash": "47e6d4bd3f64b35d8abb9925b05e112fbb1356d383dc641a47f78f8e9bbeb676",
    "source_references": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 267; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000261",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000261",
    "preferred_label": "Single-Cell Feature Detection Rate",
    "normalized_label": "single_cell_feature_detection_rate",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of single-cell feature detection rate.",
    "what_it_measures": "Assesses single-cell feature detection rate using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in single-cell feature detection rate can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Single-Cell Viability; Cell-Type Annotation Confidence; Spatial Transcriptomic Registration Accuracy",
    "common_misinterpretations": "Treating single-cell feature detection rate as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000261",
    "api_endpoint_template": "/v1/metrics/BEMO:2000261/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000261_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 268,
    "source_record_hash": "1ce87bfa0e14b3c49cdf26e92f3b39ba4ce32c6192d394a99b4f3b80c80031b2",
    "source_references": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 268; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000262",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000262",
    "preferred_label": "Single-Cell Viability",
    "normalized_label": "single_cell_viability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of single-cell viability.",
    "what_it_measures": "Assesses single-cell viability using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in single-cell viability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Single-Cell Ambient RNA Burden; Single-Cell Feature Detection Rate; Cell-Type Annotation Confidence",
    "common_misinterpretations": "Treating single-cell viability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000262",
    "api_endpoint_template": "/v1/metrics/BEMO:2000262/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000262_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 269,
    "source_record_hash": "faf5bedb35b3c8e6f9b571b29c9788bb087192d600f7d5646da266201f76f5dd",
    "source_references": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 269; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000263",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000263",
    "preferred_label": "Spatial Transcriptomic Registration Accuracy",
    "normalized_label": "spatial_transcriptomic_registration_accuracy",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The closeness of spatial transcriptomic registration to the accepted reference or true value.",
    "what_it_measures": "Assesses spatial transcriptomic registration accuracy using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in spatial transcriptomic registration accuracy can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Cell-Type Annotation Confidence; Cross-Platform Genomic Concordance",
    "common_misinterpretations": "Treating spatial transcriptomic registration accuracy as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000263",
    "api_endpoint_template": "/v1/metrics/BEMO:2000263/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000263_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 270,
    "source_record_hash": "e61d8e9d42dcb8b644bc33652bdf4f396f77ace1c2d848fb684d0c722e5a1598",
    "source_references": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 270; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000264",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000264",
    "preferred_label": "Strand Bias",
    "normalized_label": "strand_bias",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of strand bias.",
    "what_it_measures": "Assesses strand bias using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in strand bias can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Read- and variant-level quality-control summaries; replicate concordance; orthogonal confirmation; benchmarking against reference materials.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Allelic Balance; Reference Bias; Call-Rate Completeness",
    "common_misinterpretations": "Treating strand bias as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000264",
    "api_endpoint_template": "/v1/metrics/BEMO:2000264/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000264_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 271,
    "source_record_hash": "6ac08afc8cf99d9cd5ee94bc247ff32edf260fc542fd5e27409d9c3b702afd66",
    "source_references": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 271; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000265",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000265",
    "preferred_label": "Transcript Quantification Reliability",
    "normalized_label": "transcript_quantification_reliability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of transcript quantification reliability.",
    "what_it_measures": "Assesses transcript quantification reliability using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in transcript quantification reliability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Normalization Adequacy; Alternative Splicing Validation; Single-Cell Doublet Burden",
    "common_misinterpretations": "Treating transcript quantification reliability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000265",
    "api_endpoint_template": "/v1/metrics/BEMO:2000265/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000265_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 272,
    "source_record_hash": "45c762be688f8b3f57f3b563b58fc816d5802e731de9aee9acb732eea429ea1a",
    "source_references": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 272; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000266",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000266",
    "preferred_label": "Variant Call Quality",
    "normalized_label": "variant_call_quality",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100010",
    "category_label": "Genomics and Transcriptomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100010",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of variant call quality.",
    "what_it_measures": "Assesses variant call quality using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in variant call quality can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "ClinGen/ACMG evidence scoring; pedigree analysis; population databases; case-control data; functional assays; expert-panel review.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "related_frameworks_source": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA",
    "closely_related_metrics_source": "Sex Concordance; Genotype Quality; Allelic Balance",
    "common_misinterpretations": "Treating variant call quality as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies",
    "domain_applicability": "Genomics and Transcriptomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000266",
    "api_endpoint_template": "/v1/metrics/BEMO:2000266/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000266_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 273,
    "source_record_hash": "45320c5b96fc37b8148ee2721453c92e6bec79491a4ed2d2f6fedbc2cb99cb01",
    "source_references": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 273; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.equator-network.org/reporting-guidelines/strobe-me/ | https://www.ga4gh.org/ | https://www.humancellatlas.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000267",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000267",
    "preferred_label": "Accuracy",
    "normalized_label": "accuracy",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The closeness of accuracy to the accepted reference or true value.",
    "what_it_measures": "Assesses accuracy using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in accuracy can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Analytical Validity; Trueness; Analytical Precision",
    "common_misinterpretations": "Treating accuracy as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000267",
    "api_endpoint_template": "/v1/metrics/BEMO:2000267/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000267_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 274,
    "source_record_hash": "35d988975cf78a06cb70788f89a4196551552de36a3cf47e57d2d96fc8cf41fd",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 274; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000268",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000268",
    "preferred_label": "Analytical Measurement Range",
    "normalized_label": "analytical_measurement_range",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of analytical measurement range.",
    "what_it_measures": "Assesses analytical measurement range using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in analytical measurement range can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Method- and analyte-specific physical units",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Linearity; Reportable Range; Dynamic Range",
    "common_misinterpretations": "Treating analytical measurement range as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "PhysicalMeasurementScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Method- and analyte-specific physical units",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ValidatedMeasurementProcedure",
    "computation_readiness": "DomainProtocolRequired",
    "formula_status": "MethodSpecificProtocolRequired",
    "human_readable_formula": "Apply a validated analyte- and method-specific measurement procedure with calibration and quality control.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"unitRef\":\"REQUIRED\"}",
    "required_inputs": "specimen_or_material; measurement_procedure; calibration_reference; quality_control_results; unit",
    "optional_inputs": "replicate_measurements; environmental_conditions; instrument_version",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "validated assay measurement",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000268",
    "api_endpoint_template": "/v1/metrics/BEMO:2000268/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000268_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 275,
    "source_record_hash": "40562e2bdf0f0c373312aa0a75941fd6a83f056ba5201b300a46242b3f5457df",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 275; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000269",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000269",
    "preferred_label": "Analytical Precision",
    "normalized_label": "analytical_precision",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The closeness of repeated estimates or measurements and the narrowness of uncertainty around analytical.",
    "what_it_measures": "Assesses analytical precision using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in analytical precision can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Trueness; Repeatability; Intermediate Precision",
    "common_misinterpretations": "Treating analytical precision as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000269",
    "api_endpoint_template": "/v1/metrics/BEMO:2000269/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000269_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
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    "source_record_hash": "7c4987f5f8c3c9cca41bb28896f2392e5c664fc505d3f5db2c63ad7c10e1d04d",
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    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 276; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000270",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000270",
    "preferred_label": "Analytical Sensitivity",
    "normalized_label": "analytical_sensitivity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of analytical sensitivity.",
    "what_it_measures": "Assesses analytical sensitivity using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in analytical sensitivity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified threshold; valid reference standard; complete 2×2 classification; confidence intervals; spectrum and prevalence assessment.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Reproducibility of Measurement; Analytical Specificity; Limit of Detection",
    "common_misinterpretations": "Treating analytical sensitivity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
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    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000270",
    "api_endpoint_template": "/v1/metrics/BEMO:2000270/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000270_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
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    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 277; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
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  {
    "metric_id": "BEMO:2000271",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000271",
    "preferred_label": "Analytical Specificity",
    "normalized_label": "analytical_specificity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
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    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of analytical specificity.",
    "what_it_measures": "Assesses analytical specificity using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in analytical specificity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified threshold; valid reference standard; complete 2×2 classification; confidence intervals; spectrum and prevalence assessment.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Analytical Sensitivity; Limit of Detection; Limit of Quantification",
    "common_misinterpretations": "Treating analytical specificity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
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    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000271",
    "api_endpoint_template": "/v1/metrics/BEMO:2000271/compute",
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    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000271_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
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    "source_record_hash": "f6458dae6787eecc6dbfe775e26236c89d02f80c2f92e3575c7f9ddfa0e84b0e",
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    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 278; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
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  {
    "metric_id": "BEMO:2000272",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000272",
    "preferred_label": "Analytical Validity",
    "normalized_label": "analytical_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
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    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
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    "what_it_measures": "Assesses analytical validity using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in analytical validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Accuracy; Trueness",
    "common_misinterpretations": "Treating analytical validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000272",
    "api_endpoint_template": "/v1/metrics/BEMO:2000272/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000272_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 279,
    "source_record_hash": "e4b1deae92fd2c549054f6f19f234dbf0b73ab8ff30ff5741db1c88b5618f6c3",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 279; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000273",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000273",
    "preferred_label": "Batch-Effect Sensitivity",
    "normalized_label": "batch_effect_sensitivity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of batch-effect sensitivity.",
    "what_it_measures": "Assesses batch-effect sensitivity using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in batch-effect sensitivity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified threshold; valid reference standard; complete 2×2 classification; confidence intervals; spectrum and prevalence assessment.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Site-to-Site Assay Portability; Preanalytical Robustness; Postanalytical Integrity",
    "common_misinterpretations": "Treating batch-effect sensitivity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000273",
    "api_endpoint_template": "/v1/metrics/BEMO:2000273/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000273_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 280,
    "source_record_hash": "7222c30713cc035f86bae406549aaf0d4751a919d50ae68b917efd9629244d28",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 280; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000274",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000274",
    "preferred_label": "Calibration Traceability",
    "normalized_label": "calibration_traceability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of calibration traceability.",
    "what_it_measures": "Assesses calibration traceability using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in calibration traceability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Hook Effect Risk; Reference Interval Validity; Cutoff Validity",
    "common_misinterpretations": "Treating calibration traceability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000274",
    "api_endpoint_template": "/v1/metrics/BEMO:2000274/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000274_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 281,
    "source_record_hash": "7d6efe540a48fdb6c1d86b381d867ad016fd03d3ba3039e34ba0dd8d59bcbf8d",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 281; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000275",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000275",
    "preferred_label": "Carryover",
    "normalized_label": "carryover",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of carryover.",
    "what_it_measures": "Assesses carryover using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in carryover can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Replicate dilution series; blank and spiked samples; reference materials; method-comparison studies; predefined CLSI/ISO acceptance criteria.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Cross-Reactivity; Hook Effect Risk; Calibration Traceability",
    "common_misinterpretations": "Treating carryover as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000275",
    "api_endpoint_template": "/v1/metrics/BEMO:2000275/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000275_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 282,
    "source_record_hash": "0e987b7e93f5f6b586140ce3b08eb3d87acd863bc4cb825ee0d1e4b7b1bb3994",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 282; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000276",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000276",
    "preferred_label": "Commutability",
    "normalized_label": "commutability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of commutability.",
    "what_it_measures": "Assesses commutability using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in commutability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Method Comparison Agreement; Sample Stability; Reagent Lot Consistency",
    "common_misinterpretations": "Treating commutability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000276",
    "api_endpoint_template": "/v1/metrics/BEMO:2000276/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000276_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 283,
    "source_record_hash": "0d8876821c8ce33e4a6f72fcdd334c759d21fb2784bd7f9f779179758d7849c8",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 283; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000277",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000277",
    "preferred_label": "Cross-Reactivity",
    "normalized_label": "cross_reactivity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of cross-reactivity.",
    "what_it_measures": "Assesses cross-reactivity using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in cross-reactivity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Interference Susceptibility; Carryover; Hook Effect Risk",
    "common_misinterpretations": "Treating cross-reactivity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000277",
    "api_endpoint_template": "/v1/metrics/BEMO:2000277/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000277_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 284,
    "source_record_hash": "1de0ffae2d83059ba1d111ea3bf309f20078d963ac7b7f912a42e8b4e10e5e32",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 284; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000278",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000278",
    "preferred_label": "Cutoff Validity",
    "normalized_label": "cutoff_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which cutoff supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses cutoff validity using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in cutoff validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Reference Interval Validity; Measurement Uncertainty; Method Comparison Agreement",
    "common_misinterpretations": "Treating cutoff validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000278",
    "api_endpoint_template": "/v1/metrics/BEMO:2000278/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000278_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 285,
    "source_record_hash": "f74e484a95fd67b9bd73e0f0c112bc85ddaf01e7476f82b9c24c9382fe2bfe48",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 285; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000279",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000279",
    "preferred_label": "Dilution Integrity",
    "normalized_label": "dilution_integrity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of dilution integrity.",
    "what_it_measures": "Assesses dilution integrity using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in dilution integrity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Recovery; Matrix Effect; Interference Susceptibility",
    "common_misinterpretations": "Treating dilution integrity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000279",
    "api_endpoint_template": "/v1/metrics/BEMO:2000279/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000279_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 286,
    "source_record_hash": "a31ef0b724223ebc3d1ad0dbe731b0b7823f6b347840ea43769f01a33866757b",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 286; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000280",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000280",
    "preferred_label": "Dynamic Range",
    "normalized_label": "dynamic_range",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of dynamic range.",
    "what_it_measures": "Assesses dynamic range using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in dynamic range can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Method- and analyte-specific physical units",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Reportable Range; Recovery; Dilution Integrity",
    "common_misinterpretations": "Treating dynamic range as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "PhysicalMeasurementScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Method- and analyte-specific physical units",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ValidatedMeasurementProcedure",
    "computation_readiness": "DomainProtocolRequired",
    "formula_status": "MethodSpecificProtocolRequired",
    "human_readable_formula": "Apply a validated analyte- and method-specific measurement procedure with calibration and quality control.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"unitRef\":\"REQUIRED\"}",
    "required_inputs": "specimen_or_material; measurement_procedure; calibration_reference; quality_control_results; unit",
    "optional_inputs": "replicate_measurements; environmental_conditions; instrument_version",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "validated assay measurement",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000280",
    "api_endpoint_template": "/v1/metrics/BEMO:2000280/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000280_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 287,
    "source_record_hash": "41309e5f36c397d08d76621c273137352b099c93484f2a2eca025bcf85ccffdc",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 287; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000281",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000281",
    "preferred_label": "Hook Effect Risk",
    "normalized_label": "hook_effect_risk",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that hook effect introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses hook effect risk using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in hook effect risk can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Carryover; Calibration Traceability; Reference Interval Validity",
    "common_misinterpretations": "Treating hook effect risk as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000281",
    "api_endpoint_template": "/v1/metrics/BEMO:2000281/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000281_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 288,
    "source_record_hash": "3d6a1547d736b7a958bf1c94a2df8cb5599400f10305a91c657ae1dce184650b",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 288; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000282",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000282",
    "preferred_label": "Instrument Drift",
    "normalized_label": "instrument_drift",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of instrument drift.",
    "what_it_measures": "Assesses instrument drift using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in instrument drift can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Reagent Lot Consistency; Operator Variability; Site-to-Site Assay Portability",
    "common_misinterpretations": "Treating instrument drift as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000282",
    "api_endpoint_template": "/v1/metrics/BEMO:2000282/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000282_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 289,
    "source_record_hash": "39eec82dab659b7826d3bea8f3227e8afeb55e0f15214b02955200cb8a59a8ba",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 289; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000283",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000283",
    "preferred_label": "Interference Susceptibility",
    "normalized_label": "interference_susceptibility",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of interference susceptibility.",
    "what_it_measures": "Assesses interference susceptibility using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in interference susceptibility can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Replicate dilution series; blank and spiked samples; reference materials; method-comparison studies; predefined CLSI/ISO acceptance criteria.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Matrix Effect; Cross-Reactivity; Carryover",
    "common_misinterpretations": "Treating interference susceptibility as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000283",
    "api_endpoint_template": "/v1/metrics/BEMO:2000283/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000283_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 290,
    "source_record_hash": "af7341a32f2656e5638dc5bce7ac126974e88c78554d2916a696247ebbe11d2b",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 290; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000284",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000284",
    "preferred_label": "Intermediate Precision",
    "normalized_label": "intermediate_precision",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The closeness of repeated estimates or measurements and the narrowness of uncertainty around intermediate.",
    "what_it_measures": "Assesses intermediate precision using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in intermediate precision can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Repeatability; Reproducibility of Measurement; Analytical Sensitivity",
    "common_misinterpretations": "Treating intermediate precision as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000284",
    "api_endpoint_template": "/v1/metrics/BEMO:2000284/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000284_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 291,
    "source_record_hash": "543dc6e95f52dce066f892ad8d141154500ea9d0cf35d11564c84cc551f70c3b",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 291; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000285",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000285",
    "preferred_label": "Limit of Detection",
    "normalized_label": "limit_of_detection",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of limit of detection.",
    "what_it_measures": "Assesses limit of detection using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in limit of detection can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Replicate dilution series; blank and spiked samples; reference materials; method-comparison studies; predefined CLSI/ISO acceptance criteria.",
    "units_or_scale_source": "Method- and analyte-specific physical units",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Analytical Specificity; Limit of Quantification; Linearity",
    "common_misinterpretations": "Treating limit of detection as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "PhysicalMeasurementScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Method- and analyte-specific physical units",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ValidatedMeasurementProcedure",
    "computation_readiness": "DomainProtocolRequired",
    "formula_status": "MethodSpecificProtocolRequired",
    "human_readable_formula": "Apply a validated analyte- and method-specific measurement procedure with calibration and quality control.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"unitRef\":\"REQUIRED\"}",
    "required_inputs": "specimen_or_material; measurement_procedure; calibration_reference; quality_control_results; unit",
    "optional_inputs": "replicate_measurements; environmental_conditions; instrument_version",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "validated assay measurement",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000285",
    "api_endpoint_template": "/v1/metrics/BEMO:2000285/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000285_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 292,
    "source_record_hash": "32751f0c3f93a66c901d3c5cea950ee45482dac2a524a6e4ed0ddc20000649d1",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 292; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000286",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000286",
    "preferred_label": "Limit of Quantification",
    "normalized_label": "limit_of_quantification",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of limit of quantification.",
    "what_it_measures": "Assesses limit of quantification using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in limit of quantification can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Replicate dilution series; blank and spiked samples; reference materials; method-comparison studies; predefined CLSI/ISO acceptance criteria.",
    "units_or_scale_source": "Method- and analyte-specific physical units",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Limit of Detection; Linearity; Analytical Measurement Range",
    "common_misinterpretations": "Treating limit of quantification as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "PhysicalMeasurementScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Method- and analyte-specific physical units",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ValidatedMeasurementProcedure",
    "computation_readiness": "DomainProtocolRequired",
    "formula_status": "MethodSpecificProtocolRequired",
    "human_readable_formula": "Apply a validated analyte- and method-specific measurement procedure with calibration and quality control.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"unitRef\":\"REQUIRED\"}",
    "required_inputs": "specimen_or_material; measurement_procedure; calibration_reference; quality_control_results; unit",
    "optional_inputs": "replicate_measurements; environmental_conditions; instrument_version",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "validated assay measurement",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000286",
    "api_endpoint_template": "/v1/metrics/BEMO:2000286/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000286_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 293,
    "source_record_hash": "e110a21f976b308d8a01ff42efac55157e3af426e1182c74cf700e2fb4ce3595",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 293; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000287",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000287",
    "preferred_label": "Linearity",
    "normalized_label": "linearity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of linearity.",
    "what_it_measures": "Assesses linearity using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in linearity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Replicate dilution series; blank and spiked samples; reference materials; method-comparison studies; predefined CLSI/ISO acceptance criteria.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Limit of Quantification; Analytical Measurement Range; Reportable Range",
    "common_misinterpretations": "Treating linearity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000287",
    "api_endpoint_template": "/v1/metrics/BEMO:2000287/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000287_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 294,
    "source_record_hash": "511e3fb111714ad52a916859d22dfd9a9aa36539d615e5b295fdf52500ac32e5",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 294; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000288",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000288",
    "preferred_label": "Matrix Effect",
    "normalized_label": "matrix_effect",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of matrix effect.",
    "what_it_measures": "Assesses matrix effect using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in matrix effect can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Replicate dilution series; blank and spiked samples; reference materials; method-comparison studies; predefined CLSI/ISO acceptance criteria.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Dilution Integrity; Interference Susceptibility; Cross-Reactivity",
    "common_misinterpretations": "Treating matrix effect as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000288",
    "api_endpoint_template": "/v1/metrics/BEMO:2000288/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000288_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 295,
    "source_record_hash": "e901d4ca31939164c2ecbe0d0bed735b156c8e09a3c3f28444f5359947798b49",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 295; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000289",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000289",
    "preferred_label": "Measurement Uncertainty",
    "normalized_label": "measurement_uncertainty",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of measurement uncertainty.",
    "what_it_measures": "Assesses measurement uncertainty using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in measurement uncertainty can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Cutoff Validity; Method Comparison Agreement; Commutability",
    "common_misinterpretations": "Treating measurement uncertainty as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000289",
    "api_endpoint_template": "/v1/metrics/BEMO:2000289/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000289_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
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    "source_record_hash": "02b8d5d020f47fcd1190b0fa52a15a86a5dd04748bbf2908e8c4e87ccdb4670f",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 296; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000290",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000290",
    "preferred_label": "Method Comparison Agreement",
    "normalized_label": "method_comparison_agreement",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree of agreement in method comparison across measurements, studies, methods, populations, or biological levels.",
    "what_it_measures": "Assesses method comparison agreement using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in method comparison agreement can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Measurement Uncertainty; Commutability; Sample Stability",
    "common_misinterpretations": "Treating method comparison agreement as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
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    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000290",
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    "provenance_model": "W3C PROV-O",
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    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 297; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000291",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000291",
    "preferred_label": "Operator Variability",
    "normalized_label": "operator_variability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of operator variability.",
    "what_it_measures": "Assesses operator variability using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in operator variability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Instrument Drift; Site-to-Site Assay Portability; Batch-Effect Sensitivity",
    "common_misinterpretations": "Treating operator variability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
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    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000291",
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    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000291_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
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    "source_record_hash": "ae9e50b8f8857543ecb1eb315c23fc88dd3a028cfd40ee4377e1039431544ca0",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 298; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000292",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000292",
    "preferred_label": "Postanalytical Integrity",
    "normalized_label": "postanalytical_integrity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of postanalytical integrity.",
    "what_it_measures": "Assesses postanalytical integrity using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in postanalytical integrity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Preanalytical Robustness",
    "common_misinterpretations": "Treating postanalytical integrity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000292",
    "api_endpoint_template": "/v1/metrics/BEMO:2000292/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000292_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 299,
    "source_record_hash": "b1cf2cbf0a36602510f89d4d570874b9d2148d8bd132ef3b47e7be72655f9ff3",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 299; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000293",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000293",
    "preferred_label": "Preanalytical Robustness",
    "normalized_label": "preanalytical_robustness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of preanalytical robustness.",
    "what_it_measures": "Assesses preanalytical robustness using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in preanalytical robustness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Batch-Effect Sensitivity; Postanalytical Integrity",
    "common_misinterpretations": "Treating preanalytical robustness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000293",
    "api_endpoint_template": "/v1/metrics/BEMO:2000293/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000293_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 300,
    "source_record_hash": "b76350bac6098346689193598ba9a67fbdcf0cc16c9a9abb5e49d8238a97798b",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 300; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000294",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000294",
    "preferred_label": "Reagent Lot Consistency",
    "normalized_label": "reagent_lot_consistency",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree of agreement in reagent lot across measurements, studies, methods, populations, or biological levels.",
    "what_it_measures": "Assesses reagent lot consistency using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in reagent lot consistency can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Sample Stability; Instrument Drift; Operator Variability",
    "common_misinterpretations": "Treating reagent lot consistency as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000294",
    "api_endpoint_template": "/v1/metrics/BEMO:2000294/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000294_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 301,
    "source_record_hash": "66143063e8139ffa9de4cc6fb03a0eb1778bd92be05c901387fc7af071b0e433",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 301; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000295",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000295",
    "preferred_label": "Recovery",
    "normalized_label": "recovery",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of recovery.",
    "what_it_measures": "Assesses recovery using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in recovery can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Replicate dilution series; blank and spiked samples; reference materials; method-comparison studies; predefined CLSI/ISO acceptance criteria.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Dynamic Range; Dilution Integrity; Matrix Effect",
    "common_misinterpretations": "Treating recovery as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000295",
    "api_endpoint_template": "/v1/metrics/BEMO:2000295/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000295_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 302,
    "source_record_hash": "5e396bd1803ce209b22910e5705b5bf0dc26bd235bba5ac5c904b2514e3f7ea8",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 302; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000296",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000296",
    "preferred_label": "Reference Interval Validity",
    "normalized_label": "reference_interval_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which reference interval supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses reference interval validity using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in reference interval validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Calibration Traceability; Cutoff Validity; Measurement Uncertainty",
    "common_misinterpretations": "Treating reference interval validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000296",
    "api_endpoint_template": "/v1/metrics/BEMO:2000296/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000296_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 303,
    "source_record_hash": "3706e41c2a6c519ccdfb2643facf47ec1d2a45cc4b5b902e54040a5a53624b7e",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 303; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000297",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000297",
    "preferred_label": "Repeatability",
    "normalized_label": "repeatability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which repeatability yields concordant results under the specified repeated-analysis or repeated-measurement conditions.",
    "what_it_measures": "Assesses repeatability using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in repeatability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Analytical Precision; Intermediate Precision; Reproducibility of Measurement",
    "common_misinterpretations": "Treating repeatability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000297",
    "api_endpoint_template": "/v1/metrics/BEMO:2000297/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000297_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 304,
    "source_record_hash": "289ee6101d32dc64bb4644380815480f0d1de4b3d0512c355bf6d1bb8e30c7f2",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 304; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000298",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000298",
    "preferred_label": "Reportable Range",
    "normalized_label": "reportable_range",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of reportable range.",
    "what_it_measures": "Assesses reportable range using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in reportable range can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Method- and analyte-specific physical units",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Analytical Measurement Range; Dynamic Range; Recovery",
    "common_misinterpretations": "Treating reportable range as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "PhysicalMeasurementScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Method- and analyte-specific physical units",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ValidatedMeasurementProcedure",
    "computation_readiness": "DomainProtocolRequired",
    "formula_status": "MethodSpecificProtocolRequired",
    "human_readable_formula": "Apply a validated analyte- and method-specific measurement procedure with calibration and quality control.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"unitRef\":\"REQUIRED\"}",
    "required_inputs": "specimen_or_material; measurement_procedure; calibration_reference; quality_control_results; unit",
    "optional_inputs": "replicate_measurements; environmental_conditions; instrument_version",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "validated assay measurement",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000298",
    "api_endpoint_template": "/v1/metrics/BEMO:2000298/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000298_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 305,
    "source_record_hash": "1958a10669f076f26b0e434840fd948f2a615d7e3a768038db89230b0e148857",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 305; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000299",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000299",
    "preferred_label": "Reproducibility of Measurement",
    "normalized_label": "reproducibility_of_measurement",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which reproducibility of measurement yields concordant results under the specified repeated-analysis or repeated-measurement conditions.",
    "what_it_measures": "Assesses reproducibility of measurement using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in reproducibility of measurement can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Intermediate Precision; Analytical Sensitivity; Analytical Specificity",
    "common_misinterpretations": "Treating reproducibility of measurement as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000299",
    "api_endpoint_template": "/v1/metrics/BEMO:2000299/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000299_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 306,
    "source_record_hash": "83e10528c5f3255388bb807d6bfc99c4e2c93d4f418421fcd184c242521982d5",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 306; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000300",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000300",
    "preferred_label": "Sample Stability",
    "normalized_label": "sample_stability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of sample stability.",
    "what_it_measures": "Assesses sample stability using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in sample stability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Commutability; Reagent Lot Consistency; Instrument Drift",
    "common_misinterpretations": "Treating sample stability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000300",
    "api_endpoint_template": "/v1/metrics/BEMO:2000300/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000300_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 307,
    "source_record_hash": "42f10127b0bb2f21e12bfaaba11ee2a6c8335cd39935669d6733741eadfc7015",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 307; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000301",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000301",
    "preferred_label": "Site-to-Site Assay Portability",
    "normalized_label": "site_to_site_assay_portability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of site-to-site assay portability.",
    "what_it_measures": "Assesses site-to-site assay portability using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in site-to-site assay portability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Operator Variability; Batch-Effect Sensitivity; Preanalytical Robustness",
    "common_misinterpretations": "Treating site-to-site assay portability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000301",
    "api_endpoint_template": "/v1/metrics/BEMO:2000301/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000301_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 308,
    "source_record_hash": "c0e7317023f6c1fc290d021e4b38163503a72ee411cc671fe6aae25ee84d1ee5",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 308; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000302",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000302",
    "preferred_label": "Trueness",
    "normalized_label": "trueness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000003",
    "pillar_label": "Measurement, Assay, and Biospecimen Quality",
    "category_id": "BEMO:1100011",
    "category_label": "Measurement and Assay Analytical Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100011",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of trueness.",
    "what_it_measures": "Assesses trueness using evidence appropriate to measurement and assay analytical validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in trueness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Specimen / assay / run / laboratory / study",
    "applicable_study_types_source": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "related_frameworks_source": "FDA Biomarker; CLSI; ISO 15189; MIQE",
    "closely_related_metrics_source": "Accuracy; Analytical Precision; Repeatability",
    "common_misinterpretations": "Treating trueness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Specimen / assay / run / laboratory / study",
    "study_type_applicability": "Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies",
    "domain_applicability": "Measurement and Assay Analytical Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000302",
    "api_endpoint_template": "/v1/metrics/BEMO:2000302/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000302_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 309,
    "source_record_hash": "9094cf98fb975c34384185560acacc946dab62ebd8f1815100dcaac099d9df1b",
    "source_references": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 309; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.fda.gov/media/119271/download | https://clsi.org/standards/products/method-evaluation/ | https://www.iso.org/standard/76677.html | https://pubmed.ncbi.nlm.nih.gov/19246619/",
    "obo_subset": "bemo_measurement_assay_and_biospecimen_quality",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000303",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000303",
    "preferred_label": "Cross-Layer Directional Concordance",
    "normalized_label": "cross_layer_directional_concordance",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100012",
    "category_label": "Multi-omics and Systems Biology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100012",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree of agreement in cross-layer directional across measurements, studies, methods, populations, or biological levels.",
    "what_it_measures": "Assesses cross-layer directional concordance using evidence appropriate to multi-omics and systems biology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in cross-layer directional concordance can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Dataset / model / pathway / network / evidence body",
    "applicable_study_types_source": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "related_frameworks_source": "Gene Ontology; Reactome; UniProt; GA4GH",
    "closely_related_metrics_source": "Cross-Omics Replication; Latent-Factor Stability; Network Reconstruction Robustness",
    "common_misinterpretations": "Treating cross-layer directional concordance as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Dataset / model / pathway / network / evidence body",
    "study_type_applicability": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "domain_applicability": "Multi-omics and Systems Biology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000303",
    "api_endpoint_template": "/v1/metrics/BEMO:2000303/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000303_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 310,
    "source_record_hash": "89f675805a18a02e8214d03853d6a7cdcea2d29079ee839babae7605cea7a581",
    "source_references": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 310; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000304",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000304",
    "preferred_label": "Cross-Omics Integration Coherence",
    "normalized_label": "cross_omics_integration_coherence",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100012",
    "category_label": "Multi-omics and Systems Biology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100012",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of cross-omics integration coherence.",
    "what_it_measures": "Assesses cross-omics integration coherence using evidence appropriate to multi-omics and systems biology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in cross-omics integration coherence can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Dataset / model / pathway / network / evidence body",
    "applicable_study_types_source": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "related_frameworks_source": "Gene Ontology; Reactome; UniProt; GA4GH",
    "closely_related_metrics_source": "Cross-Omics Replication; Cross-Layer Directional Concordance",
    "common_misinterpretations": "Treating cross-omics integration coherence as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Developing",
    "references_source": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Developing; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Dataset / model / pathway / network / evidence body",
    "study_type_applicability": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "domain_applicability": "Multi-omics and Systems Biology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000304",
    "api_endpoint_template": "/v1/metrics/BEMO:2000304/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000304_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 311,
    "source_record_hash": "c10b406fc4ce6db5663280fc4b358cc062cc17f0ce7a593af68a762307815cdc",
    "source_references": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 311; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000305",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000305",
    "preferred_label": "Cross-Omics Replication",
    "normalized_label": "cross_omics_replication",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
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    "category_label": "Multi-omics and Systems Biology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100012",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of cross-omics replication.",
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    "why_it_matters": "Material weakness in cross-omics replication can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
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    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Dataset / model / pathway / network / evidence body",
    "applicable_study_types_source": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "related_frameworks_source": "Gene Ontology; Reactome; UniProt; GA4GH",
    "closely_related_metrics_source": "Cross-Omics Integration Coherence; Cross-Layer Directional Concordance; Latent-Factor Stability",
    "common_misinterpretations": "Treating cross-omics replication as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Developing",
    "references_source": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Developing; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Dataset / model / pathway / network / evidence body",
    "study_type_applicability": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "domain_applicability": "Multi-omics and Systems Biology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000305",
    "api_endpoint_template": "/v1/metrics/BEMO:2000305/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000305_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 312,
    "source_record_hash": "5b9be25d7af680eef194d1d2e393dbdeaaf607f62c516cb41c75f5dfd1ba50b9",
    "source_references": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 312; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
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  {
    "metric_id": "BEMO:2000306",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000306",
    "preferred_label": "Dynamical Stability",
    "normalized_label": "dynamical_stability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100012",
    "category_label": "Multi-omics and Systems Biology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100012",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of dynamical stability.",
    "what_it_measures": "Assesses dynamical stability using evidence appropriate to multi-omics and systems biology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in dynamical stability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Dataset / model / pathway / network / evidence body",
    "applicable_study_types_source": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "related_frameworks_source": "Gene Ontology; Reactome; UniProt; GA4GH",
    "closely_related_metrics_source": "Practical Identifiability; Steady-State Validity; Flux-Balance Consistency",
    "common_misinterpretations": "Treating dynamical stability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
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    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000306",
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    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
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    "source_references": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 313; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
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    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
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    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
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  {
    "metric_id": "BEMO:2000307",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000307",
    "preferred_label": "Emergent-Property Reproducibility",
    "normalized_label": "emergent_property_reproducibility",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
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    "category_id": "BEMO:1100012",
    "category_label": "Multi-omics and Systems Biology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100012",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
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    "lifecycle_status": "Candidate",
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    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which emergent-property reproducibility yields concordant results under the specified repeated-analysis or repeated-measurement conditions.",
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    "why_it_matters": "Material weakness in emergent-property reproducibility can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
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    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
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    "applicable_study_types_source": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
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    "closely_related_metrics_source": "Perturbation Prediction Accuracy",
    "common_misinterpretations": "Treating emergent-property reproducibility as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Specialized / infrequent",
    "maturity_of_metric": "Developing",
    "references_source": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
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    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
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    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
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    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Developing; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
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    "study_type_applicability": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "domain_applicability": "Multi-omics and Systems Biology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000307",
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    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000307_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
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    "source_record_hash": "e554ab3ba02f294f767076d372c3967762b850eccc356bf4d7c243480641cd98",
    "source_references": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 314; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000308",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000308",
    "preferred_label": "Entity Resolution Accuracy",
    "normalized_label": "entity_resolution_accuracy",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100012",
    "category_label": "Multi-omics and Systems Biology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100012",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The closeness of entity resolution to the accepted reference or true value.",
    "what_it_measures": "Assesses entity resolution accuracy using evidence appropriate to multi-omics and systems biology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in entity resolution accuracy can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Dataset / model / pathway / network / evidence body",
    "applicable_study_types_source": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "related_frameworks_source": "Gene Ontology; Reactome; UniProt; GA4GH",
    "closely_related_metrics_source": "Knowledge-Graph Provenance Quality; Relation Evidence Strength; Ontology Annotation Completeness",
    "common_misinterpretations": "Treating entity resolution accuracy as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Dataset / model / pathway / network / evidence body",
    "study_type_applicability": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "domain_applicability": "Multi-omics and Systems Biology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000308",
    "api_endpoint_template": "/v1/metrics/BEMO:2000308/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000308_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 315,
    "source_record_hash": "81ae3d3ac205c8d1258be22f4b5818a5c36df354b19605060eb458cfdfef682e",
    "source_references": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 315; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000309",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000309",
    "preferred_label": "Flux-Balance Consistency",
    "normalized_label": "flux_balance_consistency",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100012",
    "category_label": "Multi-omics and Systems Biology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100012",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree of agreement in flux-balance across measurements, studies, methods, populations, or biological levels.",
    "what_it_measures": "Assesses flux-balance consistency using evidence appropriate to multi-omics and systems biology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in flux-balance consistency can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Dataset / model / pathway / network / evidence body",
    "applicable_study_types_source": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "related_frameworks_source": "Gene Ontology; Reactome; UniProt; GA4GH",
    "closely_related_metrics_source": "Steady-State Validity; Perturbation Prediction Accuracy; Emergent-Property Reproducibility",
    "common_misinterpretations": "Treating flux-balance consistency as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Dataset / model / pathway / network / evidence body",
    "study_type_applicability": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "domain_applicability": "Multi-omics and Systems Biology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000309",
    "api_endpoint_template": "/v1/metrics/BEMO:2000309/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000309_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 316,
    "source_record_hash": "f8d3b19efd68e0150e437c71bac90ab2bb80f33877b4a0e74bc52542a0fd3c26",
    "source_references": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 316; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000310",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000310",
    "preferred_label": "Knowledge-Graph Evidence Completeness",
    "normalized_label": "knowledge_graph_evidence_completeness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100012",
    "category_label": "Multi-omics and Systems Biology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100012",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which all scientifically necessary components of knowledge-graph evidence are present, documented, and evaluable.",
    "what_it_measures": "Assesses knowledge-graph evidence completeness using evidence appropriate to multi-omics and systems biology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in knowledge-graph evidence completeness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Dataset / model / pathway / network / evidence body",
    "applicable_study_types_source": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "related_frameworks_source": "Gene Ontology; Reactome; UniProt; GA4GH",
    "closely_related_metrics_source": "Pathway Topology Support; Knowledge-Graph Provenance Quality; Entity Resolution Accuracy",
    "common_misinterpretations": "Treating knowledge-graph evidence completeness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Developing",
    "references_source": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Developing; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Dataset / model / pathway / network / evidence body",
    "study_type_applicability": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "domain_applicability": "Multi-omics and Systems Biology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000310",
    "api_endpoint_template": "/v1/metrics/BEMO:2000310/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000310_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 317,
    "source_record_hash": "082de1cac908d5d8b791ddee2974743d0e0eae71997e72080a5d978e931f8b6c",
    "source_references": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 317; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000311",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000311",
    "preferred_label": "Knowledge-Graph Provenance Quality",
    "normalized_label": "knowledge_graph_provenance_quality",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100012",
    "category_label": "Multi-omics and Systems Biology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100012",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of knowledge-graph provenance quality.",
    "what_it_measures": "Assesses knowledge-graph provenance quality using evidence appropriate to multi-omics and systems biology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in knowledge-graph provenance quality can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Dataset / model / pathway / network / evidence body",
    "applicable_study_types_source": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "related_frameworks_source": "Gene Ontology; Reactome; UniProt; GA4GH",
    "closely_related_metrics_source": "Knowledge-Graph Evidence Completeness; Entity Resolution Accuracy; Relation Evidence Strength",
    "common_misinterpretations": "Treating knowledge-graph provenance quality as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Developing",
    "references_source": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Developing; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Dataset / model / pathway / network / evidence body",
    "study_type_applicability": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "domain_applicability": "Multi-omics and Systems Biology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000311",
    "api_endpoint_template": "/v1/metrics/BEMO:2000311/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000311_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 318,
    "source_record_hash": "50aaf6749314a5ad4694891f48d60c74feaa99da022b5cc91c17f4221f0696a2",
    "source_references": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 318; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000312",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000312",
    "preferred_label": "Latent-Factor Stability",
    "normalized_label": "latent_factor_stability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100012",
    "category_label": "Multi-omics and Systems Biology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100012",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of latent-factor stability.",
    "what_it_measures": "Assesses latent-factor stability using evidence appropriate to multi-omics and systems biology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in latent-factor stability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Dataset / model / pathway / network / evidence body",
    "applicable_study_types_source": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "related_frameworks_source": "Gene Ontology; Reactome; UniProt; GA4GH",
    "closely_related_metrics_source": "Cross-Layer Directional Concordance; Network Reconstruction Robustness; Network Edge Confidence",
    "common_misinterpretations": "Treating latent-factor stability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Dataset / model / pathway / network / evidence body",
    "study_type_applicability": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "domain_applicability": "Multi-omics and Systems Biology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000312",
    "api_endpoint_template": "/v1/metrics/BEMO:2000312/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000312_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 319,
    "source_record_hash": "be1e726b2fd3735d5492ec8f375d473b36cbff860abc6d682d2065974c115c50",
    "source_references": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 319; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000313",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000313",
    "preferred_label": "Model–Experiment Concordance",
    "normalized_label": "model_experiment_concordance",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100012",
    "category_label": "Multi-omics and Systems Biology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100012",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree of agreement in model–experiment across measurements, studies, methods, populations, or biological levels.",
    "what_it_measures": "Assesses model–experiment concordance using evidence appropriate to multi-omics and systems biology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in model–experiment concordance can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Dataset / model / pathway / network / evidence body",
    "applicable_study_types_source": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "related_frameworks_source": "Gene Ontology; Reactome; UniProt; GA4GH",
    "closely_related_metrics_source": "Ontology Evidence-Code Strength; Parameter Identifiability; Parameter Sensitivity",
    "common_misinterpretations": "Treating model–experiment concordance as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Dataset / model / pathway / network / evidence body",
    "study_type_applicability": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "domain_applicability": "Multi-omics and Systems Biology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000313",
    "api_endpoint_template": "/v1/metrics/BEMO:2000313/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000313_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 320,
    "source_record_hash": "433f97851837c60d123f8a332258d7d5b3872aa7c5564c19691b4c4c00871a8b",
    "source_references": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 320; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000314",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000314",
    "preferred_label": "Module Stability",
    "normalized_label": "module_stability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100012",
    "category_label": "Multi-omics and Systems Biology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100012",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of module stability.",
    "what_it_measures": "Assesses module stability using evidence appropriate to multi-omics and systems biology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in module stability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Dataset / model / pathway / network / evidence body",
    "applicable_study_types_source": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "related_frameworks_source": "Gene Ontology; Reactome; UniProt; GA4GH",
    "closely_related_metrics_source": "Network Node Confidence; Pathway Enrichment Consistency; Pathway Topology Support",
    "common_misinterpretations": "Treating module stability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Dataset / model / pathway / network / evidence body",
    "study_type_applicability": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "domain_applicability": "Multi-omics and Systems Biology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000314",
    "api_endpoint_template": "/v1/metrics/BEMO:2000314/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000314_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 321,
    "source_record_hash": "191acd0c1abb112365dc2e82b9a1c639642c0798eb52983d078ac92e3f0fbeec",
    "source_references": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 321; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000315",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000315",
    "preferred_label": "Network Edge Confidence",
    "normalized_label": "network_edge_confidence",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100012",
    "category_label": "Multi-omics and Systems Biology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100012",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The justified degree of certainty assigned to network edge given the quantity, quality, consistency, and limitations of supporting evidence.",
    "what_it_measures": "Assesses network edge confidence using evidence appropriate to multi-omics and systems biology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in network edge confidence can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Dataset / model / pathway / network / evidence body",
    "applicable_study_types_source": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "related_frameworks_source": "Gene Ontology; Reactome; UniProt; GA4GH",
    "closely_related_metrics_source": "Network Reconstruction Robustness; Network Node Confidence; Module Stability",
    "common_misinterpretations": "Treating network edge confidence as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Dataset / model / pathway / network / evidence body",
    "study_type_applicability": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "domain_applicability": "Multi-omics and Systems Biology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000315",
    "api_endpoint_template": "/v1/metrics/BEMO:2000315/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000315_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 322,
    "source_record_hash": "6118b228a2af4e149e82150fb026ef08cdd6d05b9748a0128d6e8c14f147784c",
    "source_references": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 322; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000316",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000316",
    "preferred_label": "Network Node Confidence",
    "normalized_label": "network_node_confidence",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100012",
    "category_label": "Multi-omics and Systems Biology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100012",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The justified degree of certainty assigned to network node given the quantity, quality, consistency, and limitations of supporting evidence.",
    "what_it_measures": "Assesses network node confidence using evidence appropriate to multi-omics and systems biology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in network node confidence can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Dataset / model / pathway / network / evidence body",
    "applicable_study_types_source": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "related_frameworks_source": "Gene Ontology; Reactome; UniProt; GA4GH",
    "closely_related_metrics_source": "Network Edge Confidence; Module Stability; Pathway Enrichment Consistency",
    "common_misinterpretations": "Treating network node confidence as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Dataset / model / pathway / network / evidence body",
    "study_type_applicability": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "domain_applicability": "Multi-omics and Systems Biology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000316",
    "api_endpoint_template": "/v1/metrics/BEMO:2000316/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000316_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 323,
    "source_record_hash": "79eaf0a8e6c6fc3012d48e379c545c17d89aecf6de033d40ae6399ec89441a3b",
    "source_references": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 323; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000317",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000317",
    "preferred_label": "Network Reconstruction Robustness",
    "normalized_label": "network_reconstruction_robustness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100012",
    "category_label": "Multi-omics and Systems Biology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100012",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of network reconstruction robustness.",
    "what_it_measures": "Assesses network reconstruction robustness using evidence appropriate to multi-omics and systems biology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in network reconstruction robustness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Dataset / model / pathway / network / evidence body",
    "applicable_study_types_source": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "related_frameworks_source": "Gene Ontology; Reactome; UniProt; GA4GH",
    "closely_related_metrics_source": "Latent-Factor Stability; Network Edge Confidence; Network Node Confidence",
    "common_misinterpretations": "Treating network reconstruction robustness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Dataset / model / pathway / network / evidence body",
    "study_type_applicability": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "domain_applicability": "Multi-omics and Systems Biology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000317",
    "api_endpoint_template": "/v1/metrics/BEMO:2000317/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000317_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 324,
    "source_record_hash": "0b4f2bdfa3ccc3b3abdb67b1f3be15b6d8479743942152580ad3f1929db67d5f",
    "source_references": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 324; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000318",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000318",
    "preferred_label": "Ontology Annotation Completeness",
    "normalized_label": "ontology_annotation_completeness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100012",
    "category_label": "Multi-omics and Systems Biology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100012",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which all scientifically necessary components of ontology annotation are present, documented, and evaluable.",
    "what_it_measures": "Assesses ontology annotation completeness using evidence appropriate to multi-omics and systems biology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in ontology annotation completeness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Dataset / model / pathway / network / evidence body",
    "applicable_study_types_source": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "related_frameworks_source": "Gene Ontology; Reactome; UniProt; GA4GH",
    "closely_related_metrics_source": "Relation Evidence Strength; Ontology Evidence-Code Strength; Model–Experiment Concordance",
    "common_misinterpretations": "Treating ontology annotation completeness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Dataset / model / pathway / network / evidence body",
    "study_type_applicability": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "domain_applicability": "Multi-omics and Systems Biology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000318",
    "api_endpoint_template": "/v1/metrics/BEMO:2000318/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000318_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 325,
    "source_record_hash": "b8714924720c209e415f9bf2c9aaf707f6bf0edbbbf6ca8da11d2546f9da563d",
    "source_references": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 325; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000319",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000319",
    "preferred_label": "Ontology Evidence-Code Strength",
    "normalized_label": "ontology_evidence_code_strength",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100012",
    "category_label": "Multi-omics and Systems Biology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100012",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting ontology evidence-code.",
    "what_it_measures": "Assesses ontology evidence-code strength using evidence appropriate to multi-omics and systems biology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in ontology evidence-code strength can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Dataset / model / pathway / network / evidence body",
    "applicable_study_types_source": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "related_frameworks_source": "Gene Ontology; Reactome; UniProt; GA4GH",
    "closely_related_metrics_source": "Ontology Annotation Completeness; Model–Experiment Concordance; Parameter Identifiability",
    "common_misinterpretations": "Treating ontology evidence-code strength as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Dataset / model / pathway / network / evidence body",
    "study_type_applicability": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "domain_applicability": "Multi-omics and Systems Biology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000319",
    "api_endpoint_template": "/v1/metrics/BEMO:2000319/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000319_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 326,
    "source_record_hash": "98cc3b5d977b0d0bd7a309c477d2653f05eeb7554078021a2d0b2bf21036d891",
    "source_references": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 326; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000320",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000320",
    "preferred_label": "Parameter Identifiability",
    "normalized_label": "parameter_identifiability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100012",
    "category_label": "Multi-omics and Systems Biology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100012",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of parameter identifiability.",
    "what_it_measures": "Assesses parameter identifiability using evidence appropriate to multi-omics and systems biology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in parameter identifiability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Dataset / model / pathway / network / evidence body",
    "applicable_study_types_source": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "related_frameworks_source": "Gene Ontology; Reactome; UniProt; GA4GH",
    "closely_related_metrics_source": "Model–Experiment Concordance; Parameter Sensitivity; Structural Identifiability",
    "common_misinterpretations": "Treating parameter identifiability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Dataset / model / pathway / network / evidence body",
    "study_type_applicability": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "domain_applicability": "Multi-omics and Systems Biology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000320",
    "api_endpoint_template": "/v1/metrics/BEMO:2000320/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000320_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 327,
    "source_record_hash": "e1eaab072c302dca725ea1fb92e565c0aead2c5a6ddd49490dbfa43ad163dd03",
    "source_references": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 327; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000321",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000321",
    "preferred_label": "Parameter Sensitivity",
    "normalized_label": "parameter_sensitivity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100012",
    "category_label": "Multi-omics and Systems Biology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100012",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of parameter sensitivity.",
    "what_it_measures": "Assesses parameter sensitivity using evidence appropriate to multi-omics and systems biology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in parameter sensitivity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified threshold; valid reference standard; complete 2×2 classification; confidence intervals; spectrum and prevalence assessment.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Dataset / model / pathway / network / evidence body",
    "applicable_study_types_source": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "related_frameworks_source": "Gene Ontology; Reactome; UniProt; GA4GH",
    "closely_related_metrics_source": "Parameter Identifiability; Structural Identifiability; Practical Identifiability",
    "common_misinterpretations": "Treating parameter sensitivity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Dataset / model / pathway / network / evidence body",
    "study_type_applicability": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "domain_applicability": "Multi-omics and Systems Biology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000321",
    "api_endpoint_template": "/v1/metrics/BEMO:2000321/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000321_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 328,
    "source_record_hash": "9735c06335e80bafcbeea74ccb7b405e18e8684330b82448424f6e83ef3974ba",
    "source_references": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 328; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000322",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000322",
    "preferred_label": "Pathway Enrichment Consistency",
    "normalized_label": "pathway_enrichment_consistency",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100012",
    "category_label": "Multi-omics and Systems Biology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100012",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree of agreement in pathway enrichment across measurements, studies, methods, populations, or biological levels.",
    "what_it_measures": "Assesses pathway enrichment consistency using evidence appropriate to multi-omics and systems biology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in pathway enrichment consistency can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Dataset / model / pathway / network / evidence body",
    "applicable_study_types_source": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "related_frameworks_source": "Gene Ontology; Reactome; UniProt; GA4GH",
    "closely_related_metrics_source": "Module Stability; Pathway Topology Support; Knowledge-Graph Evidence Completeness",
    "common_misinterpretations": "Treating pathway enrichment consistency as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Dataset / model / pathway / network / evidence body",
    "study_type_applicability": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "domain_applicability": "Multi-omics and Systems Biology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000322",
    "api_endpoint_template": "/v1/metrics/BEMO:2000322/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000322_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 329,
    "source_record_hash": "d7e323b8eddcaff29fe662695a2fa9bae2a0f04120cfdf422fa3e2d1cd3b117e",
    "source_references": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 329; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000323",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000323",
    "preferred_label": "Pathway Topology Support",
    "normalized_label": "pathway_topology_support",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100012",
    "category_label": "Multi-omics and Systems Biology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100012",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting pathway topology.",
    "what_it_measures": "Assesses pathway topology support using evidence appropriate to multi-omics and systems biology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in pathway topology support can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Dataset / model / pathway / network / evidence body",
    "applicable_study_types_source": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "related_frameworks_source": "Gene Ontology; Reactome; UniProt; GA4GH",
    "closely_related_metrics_source": "Pathway Enrichment Consistency; Knowledge-Graph Evidence Completeness; Knowledge-Graph Provenance Quality",
    "common_misinterpretations": "Treating pathway topology support as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Dataset / model / pathway / network / evidence body",
    "study_type_applicability": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "domain_applicability": "Multi-omics and Systems Biology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000323",
    "api_endpoint_template": "/v1/metrics/BEMO:2000323/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000323_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 330,
    "source_record_hash": "f408d8b817c9e3179698dad395d8e94ea187b92ae192e0ab52e026106d82f40a",
    "source_references": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 330; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000324",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000324",
    "preferred_label": "Perturbation Prediction Accuracy",
    "normalized_label": "perturbation_prediction_accuracy",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100012",
    "category_label": "Multi-omics and Systems Biology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100012",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The closeness of perturbation prediction to the accepted reference or true value.",
    "what_it_measures": "Assesses perturbation prediction accuracy using evidence appropriate to multi-omics and systems biology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in perturbation prediction accuracy can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Dataset / model / pathway / network / evidence body",
    "applicable_study_types_source": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "related_frameworks_source": "Gene Ontology; Reactome; UniProt; GA4GH",
    "closely_related_metrics_source": "Flux-Balance Consistency; Emergent-Property Reproducibility",
    "common_misinterpretations": "Treating perturbation prediction accuracy as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Dataset / model / pathway / network / evidence body",
    "study_type_applicability": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "domain_applicability": "Multi-omics and Systems Biology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000324",
    "api_endpoint_template": "/v1/metrics/BEMO:2000324/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000324_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 331,
    "source_record_hash": "5cc466b3de703eb697570667c57a9230690c56d69b5cf6ec528e42740ec621e9",
    "source_references": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 331; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000325",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000325",
    "preferred_label": "Practical Identifiability",
    "normalized_label": "practical_identifiability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100012",
    "category_label": "Multi-omics and Systems Biology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100012",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of practical identifiability.",
    "what_it_measures": "Assesses practical identifiability using evidence appropriate to multi-omics and systems biology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in practical identifiability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Dataset / model / pathway / network / evidence body",
    "applicable_study_types_source": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "related_frameworks_source": "Gene Ontology; Reactome; UniProt; GA4GH",
    "closely_related_metrics_source": "Structural Identifiability; Dynamical Stability; Steady-State Validity",
    "common_misinterpretations": "Treating practical identifiability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Dataset / model / pathway / network / evidence body",
    "study_type_applicability": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "domain_applicability": "Multi-omics and Systems Biology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000325",
    "api_endpoint_template": "/v1/metrics/BEMO:2000325/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000325_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 332,
    "source_record_hash": "cb110edeb57b36960477192ea5d1484823905d046fc0f22c33bc8eb340c3c4c3",
    "source_references": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 332; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000326",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000326",
    "preferred_label": "Relation Evidence Strength",
    "normalized_label": "relation_evidence_strength",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100012",
    "category_label": "Multi-omics and Systems Biology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100012",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting relation evidence.",
    "what_it_measures": "Assesses relation evidence strength using evidence appropriate to multi-omics and systems biology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in relation evidence strength can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Dataset / model / pathway / network / evidence body",
    "applicable_study_types_source": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "related_frameworks_source": "Gene Ontology; Reactome; UniProt; GA4GH",
    "closely_related_metrics_source": "Entity Resolution Accuracy; Ontology Annotation Completeness; Ontology Evidence-Code Strength",
    "common_misinterpretations": "Treating relation evidence strength as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Dataset / model / pathway / network / evidence body",
    "study_type_applicability": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "domain_applicability": "Multi-omics and Systems Biology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000326",
    "api_endpoint_template": "/v1/metrics/BEMO:2000326/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000326_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 333,
    "source_record_hash": "9009911ac3f6266273d49aa664b528314dd25468ab2969a5c3dfb8593502a99c",
    "source_references": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 333; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000327",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000327",
    "preferred_label": "Steady-State Validity",
    "normalized_label": "steady_state_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100012",
    "category_label": "Multi-omics and Systems Biology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100012",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which steady-state supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses steady-state validity using evidence appropriate to multi-omics and systems biology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in steady-state validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Dataset / model / pathway / network / evidence body",
    "applicable_study_types_source": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "related_frameworks_source": "Gene Ontology; Reactome; UniProt; GA4GH",
    "closely_related_metrics_source": "Dynamical Stability; Flux-Balance Consistency; Perturbation Prediction Accuracy",
    "common_misinterpretations": "Treating steady-state validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Dataset / model / pathway / network / evidence body",
    "study_type_applicability": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "domain_applicability": "Multi-omics and Systems Biology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000327",
    "api_endpoint_template": "/v1/metrics/BEMO:2000327/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000327_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 334,
    "source_record_hash": "3a349724361b2712b35c94baaaa135ce8e313533d3edafc463242f1cddef411b",
    "source_references": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 334; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000328",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000328",
    "preferred_label": "Structural Identifiability",
    "normalized_label": "structural_identifiability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100012",
    "category_label": "Multi-omics and Systems Biology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100012",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of structural identifiability.",
    "what_it_measures": "Assesses structural identifiability using evidence appropriate to multi-omics and systems biology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in structural identifiability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Dataset / model / pathway / network / evidence body",
    "applicable_study_types_source": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "related_frameworks_source": "Gene Ontology; Reactome; UniProt; GA4GH",
    "closely_related_metrics_source": "Parameter Sensitivity; Practical Identifiability; Dynamical Stability",
    "common_misinterpretations": "Treating structural identifiability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Dataset / model / pathway / network / evidence body",
    "study_type_applicability": "Integrated omics, networks, pathways, mechanistic and dynamic systems models",
    "domain_applicability": "Multi-omics and Systems Biology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000328",
    "api_endpoint_template": "/v1/metrics/BEMO:2000328/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000328_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 335,
    "source_record_hash": "36fbdf592582d2c048b53d43d95edfca8afe5d6c7c93d352f32f2a7d7644cfbe",
    "source_references": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 335; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000329",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000329",
    "preferred_label": "Adverse Outcome Pathway Support",
    "normalized_label": "adverse_outcome_pathway_support",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting adverse outcome pathway.",
    "what_it_measures": "Assesses adverse outcome pathway support using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in adverse outcome pathway support can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "Toxicological Mode-of-Action Support; Organ-Specific Toxicity Evidence; Genotoxicity Evidence Strength",
    "common_misinterpretations": "Treating adverse outcome pathway support as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000329",
    "api_endpoint_template": "/v1/metrics/BEMO:2000329/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000329_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 336,
    "source_record_hash": "8935703e7b30761e4213b86ddafc1aecae0696f4523a201860d9e64493990a74",
    "source_references": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 336; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000330",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000330",
    "preferred_label": "Benchmark Dose Reliability",
    "normalized_label": "benchmark_dose_reliability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of benchmark dose reliability.",
    "what_it_measures": "Assesses benchmark dose reliability using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in benchmark dose reliability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Method- and analyte-specific physical units",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "Lowest-Observed-Adverse-Effect Level Robustness; Toxicological Mode-of-Action Support; Adverse Outcome Pathway Support",
    "common_misinterpretations": "Treating benchmark dose reliability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "PhysicalMeasurementScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Method- and analyte-specific physical units",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ValidatedMeasurementProcedure",
    "computation_readiness": "DomainProtocolRequired",
    "formula_status": "MethodSpecificProtocolRequired",
    "human_readable_formula": "Apply a validated analyte- and method-specific measurement procedure with calibration and quality control.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"unitRef\":\"REQUIRED\"}",
    "required_inputs": "specimen_or_material; measurement_procedure; calibration_reference; quality_control_results; unit",
    "optional_inputs": "replicate_measurements; environmental_conditions; instrument_version",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "validated assay measurement",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000330",
    "api_endpoint_template": "/v1/metrics/BEMO:2000330/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000330_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 337,
    "source_record_hash": "43d4a4ce7127bc52167a879f611c41413072f25e775dbe7c9446cf4028783b10",
    "source_references": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 337; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000331",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000331",
    "preferred_label": "Bioavailability",
    "normalized_label": "bioavailability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of bioavailability.",
    "what_it_measures": "Assesses bioavailability using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in bioavailability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "Pharmacodynamic Adequacy; Dose Proportionality; Time–Concentration Profile Adequacy",
    "common_misinterpretations": "Treating bioavailability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000331",
    "api_endpoint_template": "/v1/metrics/BEMO:2000331/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000331_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 338,
    "source_record_hash": "1dbec5a00f53d17cad5a3a88dd4dfde9ceab9bbbe33a898c76c7086698d1a0a2",
    "source_references": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 338; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000332",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000332",
    "preferred_label": "Carcinogenicity Evidence Strength",
    "normalized_label": "carcinogenicity_evidence_strength",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting carcinogenicity evidence.",
    "what_it_measures": "Assesses carcinogenicity evidence strength using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in carcinogenicity evidence strength can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "Genotoxicity Evidence Strength; Reproductive Toxicity Evidence Strength; Developmental Toxicity Evidence Strength",
    "common_misinterpretations": "Treating carcinogenicity evidence strength as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000332",
    "api_endpoint_template": "/v1/metrics/BEMO:2000332/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000332_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 339,
    "source_record_hash": "a171459b41fd9ad0436588a80669a48227118c77c3d87194654b56ab6dfa6ad7",
    "source_references": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 339; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000333",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000333",
    "preferred_label": "Developmental Toxicity Evidence Strength",
    "normalized_label": "developmental_toxicity_evidence_strength",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting developmental toxicity evidence.",
    "what_it_measures": "Assesses developmental toxicity evidence strength using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in developmental toxicity evidence strength can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "Reproductive Toxicity Evidence Strength; Immunotoxicity Evidence Strength; Toxicokinetic Concordance",
    "common_misinterpretations": "Treating developmental toxicity evidence strength as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000333",
    "api_endpoint_template": "/v1/metrics/BEMO:2000333/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000333_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 340,
    "source_record_hash": "f5636ed02b8746eb48d98671b027c695a8940399bff60ebeae8ca955d99bae6a",
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    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 340; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000334",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000334",
    "preferred_label": "Dose Proportionality",
    "normalized_label": "dose_proportionality",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of dose proportionality.",
    "what_it_measures": "Assesses dose proportionality using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in dose proportionality can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Method- and analyte-specific physical units",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "Bioavailability; Time–Concentration Profile Adequacy; Metabolite Coverage",
    "common_misinterpretations": "Treating dose proportionality as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "PhysicalMeasurementScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Method- and analyte-specific physical units",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ValidatedMeasurementProcedure",
    "computation_readiness": "DomainProtocolRequired",
    "formula_status": "MethodSpecificProtocolRequired",
    "human_readable_formula": "Apply a validated analyte- and method-specific measurement procedure with calibration and quality control.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"unitRef\":\"REQUIRED\"}",
    "required_inputs": "specimen_or_material; measurement_procedure; calibration_reference; quality_control_results; unit",
    "optional_inputs": "replicate_measurements; environmental_conditions; instrument_version",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "validated assay measurement",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000334",
    "api_endpoint_template": "/v1/metrics/BEMO:2000334/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000334_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 341,
    "source_record_hash": "6d7bafb114f62ee059333139662f0dfa2a0fb0aaab829ac8fcdb03ed2fbd0708",
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    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 341; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000335",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000335",
    "preferred_label": "Drug–Drug Interaction Evidence",
    "normalized_label": "drug_drug_interaction_evidence",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of drug–drug interaction evidence.",
    "what_it_measures": "Assesses drug–drug interaction evidence using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in drug–drug interaction evidence can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "Metabolite Coverage; Receptor Occupancy Evidence; Selectivity Profile",
    "common_misinterpretations": "Treating drug–drug interaction evidence as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000335",
    "api_endpoint_template": "/v1/metrics/BEMO:2000335/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000335_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 342,
    "source_record_hash": "3a82aa8a1751fa8372cd9735fd975781682a359be68aacfb1d0d78e896d96ce5",
    "source_references": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 342; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000336",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000336",
    "preferred_label": "Efficacy Reproducibility",
    "normalized_label": "efficacy_reproducibility",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which efficacy reproducibility yields concordant results under the specified repeated-analysis or repeated-measurement conditions.",
    "what_it_measures": "Assesses efficacy reproducibility using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in efficacy reproducibility can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "Potency Reproducibility; Therapeutic Window Evidence; Safety Margin Evidence",
    "common_misinterpretations": "Treating efficacy reproducibility as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000336",
    "api_endpoint_template": "/v1/metrics/BEMO:2000336/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000336_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 343,
    "source_record_hash": "e3d46320b779b7100a656dae6dcb02f7b9eae6762c1680f48b9313843cb64c84",
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    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 343; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000337",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000337",
    "preferred_label": "Exposure–Response Relationship",
    "normalized_label": "exposure_response_relationship",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of exposure–response relationship.",
    "what_it_measures": "Assesses exposure–response relationship using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in exposure–response relationship can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "Pharmacological Target Validity; Pharmacokinetic Adequacy; Pharmacodynamic Adequacy",
    "common_misinterpretations": "Treating exposure–response relationship as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000337",
    "api_endpoint_template": "/v1/metrics/BEMO:2000337/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000337_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
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    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 344; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000338",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000338",
    "preferred_label": "Genotoxicity Evidence Strength",
    "normalized_label": "genotoxicity_evidence_strength",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting genotoxicity evidence.",
    "what_it_measures": "Assesses genotoxicity evidence strength using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in genotoxicity evidence strength can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "Organ-Specific Toxicity Evidence; Carcinogenicity Evidence Strength; Reproductive Toxicity Evidence Strength",
    "common_misinterpretations": "Treating genotoxicity evidence strength as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000338",
    "api_endpoint_template": "/v1/metrics/BEMO:2000338/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000338_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 345,
    "source_record_hash": "e40592e267890e51ad35407c7dc2af7775fdac9174afe2f08486d28a5e2901b8",
    "source_references": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 345; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000339",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000339",
    "preferred_label": "Human-Relevance of Toxicological Evidence",
    "normalized_label": "human_relevance_of_toxicological_evidence",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of human-relevance of toxicological evidence.",
    "what_it_measures": "Assesses human-relevance of toxicological evidence using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in human-relevance of toxicological evidence can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "Species Extrapolation Validity; Mixture Interaction Assessment",
    "common_misinterpretations": "Treating human-relevance of toxicological evidence as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000339",
    "api_endpoint_template": "/v1/metrics/BEMO:2000339/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000339_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 346,
    "source_record_hash": "32b4aadfeeab004a7a018b1fe09f04f0b2283eb92e7749123f8ac828db8cfce6",
    "source_references": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 346; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000340",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000340",
    "preferred_label": "Immunotoxicity Evidence Strength",
    "normalized_label": "immunotoxicity_evidence_strength",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting immunotoxicity evidence.",
    "what_it_measures": "Assesses immunotoxicity evidence strength using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in immunotoxicity evidence strength can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "Developmental Toxicity Evidence Strength; Toxicokinetic Concordance; Species Extrapolation Validity",
    "common_misinterpretations": "Treating immunotoxicity evidence strength as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000340",
    "api_endpoint_template": "/v1/metrics/BEMO:2000340/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000340_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 347,
    "source_record_hash": "577a4370c7a1dc270882fc655889fdc7a0b8ee20d5e6f81f1f733233db939fbd",
    "source_references": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 347; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000341",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000341",
    "preferred_label": "Lowest-Observed-Adverse-Effect Level Robustness",
    "normalized_label": "lowest_observed_adverse_effect_level_robustness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of lowest-observed-adverse-effect level robustness.",
    "what_it_measures": "Assesses lowest-observed-adverse-effect level robustness using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in lowest-observed-adverse-effect level robustness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "No-Observed-Adverse-Effect Level Robustness; Benchmark Dose Reliability; Toxicological Mode-of-Action Support",
    "common_misinterpretations": "Treating lowest-observed-adverse-effect level robustness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000341",
    "api_endpoint_template": "/v1/metrics/BEMO:2000341/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000341_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 348,
    "source_record_hash": "cd00c7765086fbbe65040e649de98f22bdf10298c91d8da0f6e7300a18f0ba9f",
    "source_references": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 348; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000342",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000342",
    "preferred_label": "Metabolite Coverage",
    "normalized_label": "metabolite_coverage",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The proportion and representativeness of the relevant metabolite captured by the evidence or measurement process.",
    "what_it_measures": "Assesses metabolite coverage using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in metabolite coverage can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Target-decoy analysis; spectral scoring; reference standards; replicate injections; retention-time and mass-error monitoring; orthogonal confirmation.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "Time–Concentration Profile Adequacy; Drug–Drug Interaction Evidence; Receptor Occupancy Evidence",
    "common_misinterpretations": "Treating metabolite coverage as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000342",
    "api_endpoint_template": "/v1/metrics/BEMO:2000342/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000342_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 349,
    "source_record_hash": "4bb05358971c228c81cd2238f505b14da043cabfc3f68e3d2dd07884c7f72bc5",
    "source_references": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 349; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000343",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000343",
    "preferred_label": "Mixture Interaction Assessment",
    "normalized_label": "mixture_interaction_assessment",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of mixture interaction assessment.",
    "what_it_measures": "Assesses mixture interaction assessment using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in mixture interaction assessment can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "Human-Relevance of Toxicological Evidence",
    "common_misinterpretations": "Treating mixture interaction assessment as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000343",
    "api_endpoint_template": "/v1/metrics/BEMO:2000343/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000343_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 350,
    "source_record_hash": "241ffa4364ee9325fbb3832728344d8484375a1aca172f524b6f871b9dc07687",
    "source_references": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 350; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000344",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000344",
    "preferred_label": "No-Observed-Adverse-Effect Level Robustness",
    "normalized_label": "no_observed_adverse_effect_level_robustness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of no-observed-adverse-effect level robustness.",
    "what_it_measures": "Assesses no-observed-adverse-effect level robustness using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in no-observed-adverse-effect level robustness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "Safety Margin Evidence; Lowest-Observed-Adverse-Effect Level Robustness; Benchmark Dose Reliability",
    "common_misinterpretations": "Treating no-observed-adverse-effect level robustness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000344",
    "api_endpoint_template": "/v1/metrics/BEMO:2000344/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000344_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 351,
    "source_record_hash": "f5f71661574e809d9eb1b7625ffde603665b4c0d25ddbb968f6b8d1a88c38a42",
    "source_references": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 351; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000345",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000345",
    "preferred_label": "Organ-Specific Toxicity Evidence",
    "normalized_label": "organ_specific_toxicity_evidence",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of organ-specific toxicity evidence.",
    "what_it_measures": "Assesses organ-specific toxicity evidence using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in organ-specific toxicity evidence can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "Adverse Outcome Pathway Support; Genotoxicity Evidence Strength; Carcinogenicity Evidence Strength",
    "common_misinterpretations": "Treating organ-specific toxicity evidence as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000345",
    "api_endpoint_template": "/v1/metrics/BEMO:2000345/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000345_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 352,
    "source_record_hash": "277a918d22b52db9e79eabf5451f64320f342f326be1cc2382f16c69ec72f0a9",
    "source_references": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 352; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000346",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000346",
    "preferred_label": "Pharmacodynamic Adequacy",
    "normalized_label": "pharmacodynamic_adequacy",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which pharmacodynamic is sufficient and fit for the stated biomedical inference.",
    "what_it_measures": "Assesses pharmacodynamic adequacy using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in pharmacodynamic adequacy can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "Pharmacokinetic Adequacy; Bioavailability; Dose Proportionality",
    "common_misinterpretations": "Treating pharmacodynamic adequacy as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000346",
    "api_endpoint_template": "/v1/metrics/BEMO:2000346/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000346_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 353,
    "source_record_hash": "99eef93672d2993b0ec131c09788c14463fd2a5166870e81b6b8d81c3637506b",
    "source_references": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 353; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000347",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000347",
    "preferred_label": "Pharmacokinetic Adequacy",
    "normalized_label": "pharmacokinetic_adequacy",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which pharmacokinetic is sufficient and fit for the stated biomedical inference.",
    "what_it_measures": "Assesses pharmacokinetic adequacy using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in pharmacokinetic adequacy can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "Exposure–Response Relationship; Pharmacodynamic Adequacy; Bioavailability",
    "common_misinterpretations": "Treating pharmacokinetic adequacy as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000347",
    "api_endpoint_template": "/v1/metrics/BEMO:2000347/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000347_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 354,
    "source_record_hash": "2b02efdd0f6a774096cee910d90b575b8f28f136a8ee594876642fb213f66330",
    "source_references": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 354; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000348",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000348",
    "preferred_label": "Pharmacological Target Validity",
    "normalized_label": "pharmacological_target_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which pharmacological target supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses pharmacological target validity using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in pharmacological target validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "Exposure–Response Relationship; Pharmacokinetic Adequacy",
    "common_misinterpretations": "Treating pharmacological target validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000348",
    "api_endpoint_template": "/v1/metrics/BEMO:2000348/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000348_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 355,
    "source_record_hash": "2cff4752043ea892788f37639d922b1a249d83c13dfedf581ad1a4ad12ab95b8",
    "source_references": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 355; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000349",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000349",
    "preferred_label": "Potency Reproducibility",
    "normalized_label": "potency_reproducibility",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which potency reproducibility yields concordant results under the specified repeated-analysis or repeated-measurement conditions.",
    "what_it_measures": "Assesses potency reproducibility using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in potency reproducibility can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "Selectivity Profile; Efficacy Reproducibility; Therapeutic Window Evidence",
    "common_misinterpretations": "Treating potency reproducibility as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000349",
    "api_endpoint_template": "/v1/metrics/BEMO:2000349/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000349_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 356,
    "source_record_hash": "2199b92ac6c23ce1866fa6fdae782c65a478ec51834e2f0193f79d608ea4c3e7",
    "source_references": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 356; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000350",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000350",
    "preferred_label": "Receptor Occupancy Evidence",
    "normalized_label": "receptor_occupancy_evidence",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of receptor occupancy evidence.",
    "what_it_measures": "Assesses receptor occupancy evidence using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in receptor occupancy evidence can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "Drug–Drug Interaction Evidence; Selectivity Profile; Potency Reproducibility",
    "common_misinterpretations": "Treating receptor occupancy evidence as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000350",
    "api_endpoint_template": "/v1/metrics/BEMO:2000350/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000350_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 357,
    "source_record_hash": "5025e34702ce03c8ed7e7aa3ed95dd9bde6bac1786183651ce608b34ffcc6a28",
    "source_references": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 357; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000351",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000351",
    "preferred_label": "Reproductive Toxicity Evidence Strength",
    "normalized_label": "reproductive_toxicity_evidence_strength",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting reproductive toxicity evidence.",
    "what_it_measures": "Assesses reproductive toxicity evidence strength using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in reproductive toxicity evidence strength can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "Carcinogenicity Evidence Strength; Developmental Toxicity Evidence Strength; Immunotoxicity Evidence Strength",
    "common_misinterpretations": "Treating reproductive toxicity evidence strength as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000351",
    "api_endpoint_template": "/v1/metrics/BEMO:2000351/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000351_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 358,
    "source_record_hash": "1725f0845040d88689ff2869cde10ea44454b5cfaa1c303d02071f7ff5ccb751",
    "source_references": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 358; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000352",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000352",
    "preferred_label": "Safety Margin Evidence",
    "normalized_label": "safety_margin_evidence",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of safety margin evidence.",
    "what_it_measures": "Assesses safety margin evidence using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in safety margin evidence can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "Therapeutic Window Evidence; No-Observed-Adverse-Effect Level Robustness; Lowest-Observed-Adverse-Effect Level Robustness",
    "common_misinterpretations": "Treating safety margin evidence as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000352",
    "api_endpoint_template": "/v1/metrics/BEMO:2000352/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000352_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 359,
    "source_record_hash": "51ce0324d6952becbbadfd71ba2913a1f56afbcc33aa0148093d10994d18697d",
    "source_references": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 359; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000353",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000353",
    "preferred_label": "Selectivity Profile",
    "normalized_label": "selectivity_profile",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of selectivity profile.",
    "what_it_measures": "Assesses selectivity profile using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in selectivity profile can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "Receptor Occupancy Evidence; Potency Reproducibility; Efficacy Reproducibility",
    "common_misinterpretations": "Treating selectivity profile as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000353",
    "api_endpoint_template": "/v1/metrics/BEMO:2000353/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000353_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 360,
    "source_record_hash": "2957579a3d734fc808c8a89eb160fb182b5f5a0f68ba40c4eecc1921dea93153",
    "source_references": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 360; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000354",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000354",
    "preferred_label": "Species Extrapolation Validity",
    "normalized_label": "species_extrapolation_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which species extrapolation supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses species extrapolation validity using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in species extrapolation validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "Toxicokinetic Concordance; Human-Relevance of Toxicological Evidence; Mixture Interaction Assessment",
    "common_misinterpretations": "Treating species extrapolation validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000354",
    "api_endpoint_template": "/v1/metrics/BEMO:2000354/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000354_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 361,
    "source_record_hash": "f3eb077ab3d21773df18d06eb29c8a11272ed7cbfe8f22da0ffedd8a171bc393",
    "source_references": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 361; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000355",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000355",
    "preferred_label": "Therapeutic Window Evidence",
    "normalized_label": "therapeutic_window_evidence",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of therapeutic window evidence.",
    "what_it_measures": "Assesses therapeutic window evidence using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in therapeutic window evidence can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "Efficacy Reproducibility; Safety Margin Evidence; No-Observed-Adverse-Effect Level Robustness",
    "common_misinterpretations": "Treating therapeutic window evidence as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000355",
    "api_endpoint_template": "/v1/metrics/BEMO:2000355/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000355_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 362,
    "source_record_hash": "34f5d4730ddbb7e269fc6713d96c49c0fba2d2f738ddbfb47d339a6ed5f8cf6e",
    "source_references": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 362; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000356",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000356",
    "preferred_label": "Time–Concentration Profile Adequacy",
    "normalized_label": "time_concentration_profile_adequacy",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which time–concentration profile is sufficient and fit for the stated biomedical inference.",
    "what_it_measures": "Assesses time–concentration profile adequacy using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in time–concentration profile adequacy can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Method- and analyte-specific physical units",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "Dose Proportionality; Metabolite Coverage; Drug–Drug Interaction Evidence",
    "common_misinterpretations": "Treating time–concentration profile adequacy as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "PhysicalMeasurementScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Method- and analyte-specific physical units",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ValidatedMeasurementProcedure",
    "computation_readiness": "DomainProtocolRequired",
    "formula_status": "MethodSpecificProtocolRequired",
    "human_readable_formula": "Apply a validated analyte- and method-specific measurement procedure with calibration and quality control.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"unitRef\":\"REQUIRED\"}",
    "required_inputs": "specimen_or_material; measurement_procedure; calibration_reference; quality_control_results; unit",
    "optional_inputs": "replicate_measurements; environmental_conditions; instrument_version",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "validated assay measurement",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000356",
    "api_endpoint_template": "/v1/metrics/BEMO:2000356/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000356_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 363,
    "source_record_hash": "8bfcea065494f7118cb14f95a9459e3f35fa404437872877955c4fdff069147a",
    "source_references": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 363; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000357",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000357",
    "preferred_label": "Toxicokinetic Concordance",
    "normalized_label": "toxicokinetic_concordance",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree of agreement in toxicokinetic across measurements, studies, methods, populations, or biological levels.",
    "what_it_measures": "Assesses toxicokinetic concordance using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in toxicokinetic concordance can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "Immunotoxicity Evidence Strength; Species Extrapolation Validity; Human-Relevance of Toxicological Evidence",
    "common_misinterpretations": "Treating toxicokinetic concordance as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000357",
    "api_endpoint_template": "/v1/metrics/BEMO:2000357/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000357_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 364,
    "source_record_hash": "6cda2f6cb167ccc21d05523345b2fef382432ceed6ebbcbe84fa383cddc4562e",
    "source_references": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 364; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000358",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000358",
    "preferred_label": "Toxicological Mode-of-Action Support",
    "normalized_label": "toxicological_mode_of_action_support",
    "abbreviation": "",
    "pillar_id": "BEMO:1000008",
    "pillar_label": "Pharmacology and Toxicology",
    "category_id": "BEMO:1100013",
    "category_label": "Pharmacology and Toxicology",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100013",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting toxicological mode-of-action.",
    "what_it_measures": "Assesses toxicological mode-of-action support using evidence appropriate to pharmacology and toxicology, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in toxicological mode-of-action support can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "related_frameworks_source": "OECD; OHAT; FDA Biomarker; EMA E16",
    "closely_related_metrics_source": "Benchmark Dose Reliability; Adverse Outcome Pathway Support; Organ-Specific Toxicity Evidence",
    "common_misinterpretations": "Treating toxicological mode-of-action support as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies",
    "domain_applicability": "Pharmacology and Toxicology",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000358",
    "api_endpoint_template": "/v1/metrics/BEMO:2000358/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000358_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 365,
    "source_record_hash": "05b74bda1c6ce0d8b99d4d0ffdc239f28a207c0631f25d1605f8d1438c74148a",
    "source_references": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 365; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.oecd.org/chemicalsafety/testing/oecd-guidelines-testing-chemicals-related-documents.htm | https://ntp.niehs.nih.gov/whatwestudy/assessments/noncancer/handbook | https://www.fda.gov/media/119271/download | https://www.ema.europa.eu/en/ich-e16-genomic-biomarkers-related-drug-response-context-structure-format-qualification-submissions-scientific-guideline",
    "obo_subset": "bemo_pharmacology_and_toxicology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000359",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000359",
    "preferred_label": "Cross-Omics Concordance",
    "normalized_label": "cross_omics_concordance",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100014",
    "category_label": "Proteomics and Metabolomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100014",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree of agreement in cross-omics across measurements, studies, methods, populations, or biological levels.",
    "what_it_measures": "Assesses cross-omics concordance using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in cross-omics concordance can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "related_frameworks_source": "MIAPE; HUPO PSI; Metabolomics Standards",
    "closely_related_metrics_source": "Pathway Enrichment Robustness",
    "common_misinterpretations": "Treating cross-omics concordance as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Developing",
    "references_source": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Developing; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "domain_applicability": "Proteomics and Metabolomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000359",
    "api_endpoint_template": "/v1/metrics/BEMO:2000359/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000359_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 366,
    "source_record_hash": "447ad3207c1d5333015f6a5189727d810a3a517e4d6a4351f8dc28acbe93a5f0",
    "source_references": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 366; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000360",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000360",
    "preferred_label": "Derivatization Efficiency",
    "normalized_label": "derivatization_efficiency",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100014",
    "category_label": "Proteomics and Metabolomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100014",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of derivatization efficiency.",
    "what_it_measures": "Assesses derivatization efficiency using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in derivatization efficiency can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "related_frameworks_source": "MIAPE; HUPO PSI; Metabolomics Standards",
    "closely_related_metrics_source": "Extraction Recovery; Metabolic Feature Reproducibility; Pathway Enrichment Robustness",
    "common_misinterpretations": "Treating derivatization efficiency as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "domain_applicability": "Proteomics and Metabolomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000360",
    "api_endpoint_template": "/v1/metrics/BEMO:2000360/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000360_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 367,
    "source_record_hash": "d83b78fc8beda508a5c18da8dbb9e284c948a9741d4fb8d070f9f30bc9267827",
    "source_references": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 367; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000361",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000361",
    "preferred_label": "Dynamic Range Coverage",
    "normalized_label": "dynamic_range_coverage",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100014",
    "category_label": "Proteomics and Metabolomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100014",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The proportion and representativeness of the relevant dynamic range captured by the evidence or measurement process.",
    "what_it_measures": "Assesses dynamic range coverage using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in dynamic range coverage can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "related_frameworks_source": "MIAPE; HUPO PSI; Metabolomics Standards",
    "closely_related_metrics_source": "Quantification Accuracy; Missing-Value Burden; Ion Suppression Assessment",
    "common_misinterpretations": "Treating dynamic range coverage as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "domain_applicability": "Proteomics and Metabolomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000361",
    "api_endpoint_template": "/v1/metrics/BEMO:2000361/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000361_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 368,
    "source_record_hash": "57e4c77ea2a48565f0758aadf8529c7db52bab9beb67f6e9c8366f0f3232e753",
    "source_references": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 368; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000362",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000362",
    "preferred_label": "Extraction Recovery",
    "normalized_label": "extraction_recovery",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100014",
    "category_label": "Proteomics and Metabolomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100014",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of extraction recovery.",
    "what_it_measures": "Assesses extraction recovery using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in extraction recovery can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Replicate dilution series; blank and spiked samples; reference materials; method-comparison studies; predefined CLSI/ISO acceptance criteria.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "related_frameworks_source": "MIAPE; HUPO PSI; Metabolomics Standards",
    "closely_related_metrics_source": "Internal Standard Performance; Derivatization Efficiency; Metabolic Feature Reproducibility",
    "common_misinterpretations": "Treating extraction recovery as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "domain_applicability": "Proteomics and Metabolomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000362",
    "api_endpoint_template": "/v1/metrics/BEMO:2000362/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000362_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 369,
    "source_record_hash": "5024c9034e231e8bc296cf1d9092cc063fe94890f4856d8bf70ac077514b55f9",
    "source_references": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 369; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000363",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000363",
    "preferred_label": "False Discovery Rate Control",
    "normalized_label": "false_discovery_rate_control",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100014",
    "category_label": "Proteomics and Metabolomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100014",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of false discovery rate control.",
    "what_it_measures": "Assesses false discovery rate control using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in false discovery rate control can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "related_frameworks_source": "MIAPE; HUPO PSI; Metabolomics Standards",
    "closely_related_metrics_source": "Protein Identification Confidence; Peptide-Spectrum Match Quality; Protein Inference Reliability",
    "common_misinterpretations": "Treating false discovery rate control as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "domain_applicability": "Proteomics and Metabolomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000363",
    "api_endpoint_template": "/v1/metrics/BEMO:2000363/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000363_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 370,
    "source_record_hash": "4059adb92dbe8fea43e57c309bf3c42531450ae52d814c6f79932af37f2f97a2",
    "source_references": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 370; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000364",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000364",
    "preferred_label": "Fragmentation Spectrum Quality",
    "normalized_label": "fragmentation_spectrum_quality",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100014",
    "category_label": "Proteomics and Metabolomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100014",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of fragmentation spectrum quality.",
    "what_it_measures": "Assesses fragmentation spectrum quality using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in fragmentation spectrum quality can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Target-decoy analysis; spectral scoring; reference standards; replicate injections; retention-time and mass-error monitoring; orthogonal confirmation.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "related_frameworks_source": "MIAPE; HUPO PSI; Metabolomics Standards",
    "closely_related_metrics_source": "Isotope Pattern Fidelity; Post-Translational Modification Localization Confidence; Proteoform Identification Confidence",
    "common_misinterpretations": "Treating fragmentation spectrum quality as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "domain_applicability": "Proteomics and Metabolomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000364",
    "api_endpoint_template": "/v1/metrics/BEMO:2000364/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000364_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 371,
    "source_record_hash": "4295f539b87882bc52461f7bd190419d6afdf7864927b9a24efe1e5f65c9fcd7",
    "source_references": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 371; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000365",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000365",
    "preferred_label": "Internal Standard Performance",
    "normalized_label": "internal_standard_performance",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100014",
    "category_label": "Proteomics and Metabolomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100014",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of internal standard performance.",
    "what_it_measures": "Assesses internal standard performance using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in internal standard performance can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "related_frameworks_source": "MIAPE; HUPO PSI; Metabolomics Standards",
    "closely_related_metrics_source": "Spectral Library Match Quality; Extraction Recovery; Derivatization Efficiency",
    "common_misinterpretations": "Treating internal standard performance as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "domain_applicability": "Proteomics and Metabolomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000365",
    "api_endpoint_template": "/v1/metrics/BEMO:2000365/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000365_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 372,
    "source_record_hash": "904dce77d19fcc637d6eae56d2d92b19b7052fd578de120e2a18bb08d00f2f54",
    "source_references": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 372; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000366",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000366",
    "preferred_label": "Ion Suppression Assessment",
    "normalized_label": "ion_suppression_assessment",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100014",
    "category_label": "Proteomics and Metabolomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100014",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of ion suppression assessment.",
    "what_it_measures": "Assesses ion suppression assessment using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in ion suppression assessment can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "related_frameworks_source": "MIAPE; HUPO PSI; Metabolomics Standards",
    "closely_related_metrics_source": "Missing-Value Burden; Retention-Time Stability; Mass Accuracy",
    "common_misinterpretations": "Treating ion suppression assessment as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "domain_applicability": "Proteomics and Metabolomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000366",
    "api_endpoint_template": "/v1/metrics/BEMO:2000366/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000366_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 373,
    "source_record_hash": "c108ebf1ca903ed7e96063f24ecaf39723dd5e925f97d641601f89fd859897b9",
    "source_references": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 373; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000367",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000367",
    "preferred_label": "Isotope Pattern Fidelity",
    "normalized_label": "isotope_pattern_fidelity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100014",
    "category_label": "Proteomics and Metabolomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100014",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of isotope pattern fidelity.",
    "what_it_measures": "Assesses isotope pattern fidelity using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in isotope pattern fidelity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "related_frameworks_source": "MIAPE; HUPO PSI; Metabolomics Standards",
    "closely_related_metrics_source": "Mass Accuracy; Fragmentation Spectrum Quality; Post-Translational Modification Localization Confidence",
    "common_misinterpretations": "Treating isotope pattern fidelity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "domain_applicability": "Proteomics and Metabolomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000367",
    "api_endpoint_template": "/v1/metrics/BEMO:2000367/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000367_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 374,
    "source_record_hash": "beec5d62727ea3baba10451d532801205b190af60b03027284c15989d51ba1e4",
    "source_references": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 374; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000368",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000368",
    "preferred_label": "Mass Accuracy",
    "normalized_label": "mass_accuracy",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100014",
    "category_label": "Proteomics and Metabolomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100014",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The closeness of mass to the accepted reference or true value.",
    "what_it_measures": "Assesses mass accuracy using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in mass accuracy can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Target-decoy analysis; spectral scoring; reference standards; replicate injections; retention-time and mass-error monitoring; orthogonal confirmation.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "related_frameworks_source": "MIAPE; HUPO PSI; Metabolomics Standards",
    "closely_related_metrics_source": "Retention-Time Stability; Isotope Pattern Fidelity; Fragmentation Spectrum Quality",
    "common_misinterpretations": "Treating mass accuracy as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "domain_applicability": "Proteomics and Metabolomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000368",
    "api_endpoint_template": "/v1/metrics/BEMO:2000368/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000368_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 375,
    "source_record_hash": "ebb0e828e6a056d20bce6788aee10b743cfcc2fc175a82fd693585711880ff73",
    "source_references": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 375; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000369",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000369",
    "preferred_label": "Metabolic Feature Reproducibility",
    "normalized_label": "metabolic_feature_reproducibility",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100014",
    "category_label": "Proteomics and Metabolomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100014",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which metabolic feature reproducibility yields concordant results under the specified repeated-analysis or repeated-measurement conditions.",
    "what_it_measures": "Assesses metabolic feature reproducibility using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in metabolic feature reproducibility can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "related_frameworks_source": "MIAPE; HUPO PSI; Metabolomics Standards",
    "closely_related_metrics_source": "Derivatization Efficiency; Pathway Enrichment Robustness; Cross-Omics Concordance",
    "common_misinterpretations": "Treating metabolic feature reproducibility as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "domain_applicability": "Proteomics and Metabolomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000369",
    "api_endpoint_template": "/v1/metrics/BEMO:2000369/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000369_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 376,
    "source_record_hash": "521bf8b7c1bbe892685e95c05cc7d63a05c4e26119e9951d705ff460b3bb99d1",
    "source_references": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 376; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000370",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000370",
    "preferred_label": "Metabolite Annotation Level",
    "normalized_label": "metabolite_annotation_level",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100014",
    "category_label": "Proteomics and Metabolomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100014",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of metabolite annotation level.",
    "what_it_measures": "Assesses metabolite annotation level using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in metabolite annotation level can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Target-decoy analysis; spectral scoring; reference standards; replicate injections; retention-time and mass-error monitoring; orthogonal confirmation.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "related_frameworks_source": "MIAPE; HUPO PSI; Metabolomics Standards",
    "closely_related_metrics_source": "Metabolite Identification Confidence; Spectral Library Match Quality; Internal Standard Performance",
    "common_misinterpretations": "Treating metabolite annotation level as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "domain_applicability": "Proteomics and Metabolomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000370",
    "api_endpoint_template": "/v1/metrics/BEMO:2000370/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000370_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 377,
    "source_record_hash": "883e5fdd2ff9e198b3ddcbafc3e6478eed144bbcc7f46c67f19ec93850e8ec4c",
    "source_references": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 377; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000371",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000371",
    "preferred_label": "Metabolite Identification Confidence",
    "normalized_label": "metabolite_identification_confidence",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100014",
    "category_label": "Proteomics and Metabolomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100014",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The justified degree of certainty assigned to metabolite identification given the quantity, quality, consistency, and limitations of supporting evidence.",
    "what_it_measures": "Assesses metabolite identification confidence using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in metabolite identification confidence can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Target-decoy analysis; spectral scoring; reference standards; replicate injections; retention-time and mass-error monitoring; orthogonal confirmation.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "related_frameworks_source": "MIAPE; HUPO PSI; Metabolomics Standards",
    "closely_related_metrics_source": "Proteoform Identification Confidence; Metabolite Annotation Level; Spectral Library Match Quality",
    "common_misinterpretations": "Treating metabolite identification confidence as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "domain_applicability": "Proteomics and Metabolomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000371",
    "api_endpoint_template": "/v1/metrics/BEMO:2000371/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000371_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 378,
    "source_record_hash": "dd08774f62d4c8036bc0f7c590a94eca58c7ca0613c38dec0e386cab59cc0dbd",
    "source_references": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 378; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000372",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000372",
    "preferred_label": "Missing-Value Burden",
    "normalized_label": "missing_value_burden",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100014",
    "category_label": "Proteomics and Metabolomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100014",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of missing-value burden.",
    "what_it_measures": "Assesses missing-value burden using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in missing-value burden can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "related_frameworks_source": "MIAPE; HUPO PSI; Metabolomics Standards",
    "closely_related_metrics_source": "Dynamic Range Coverage; Ion Suppression Assessment; Retention-Time Stability",
    "common_misinterpretations": "Treating missing-value burden as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "domain_applicability": "Proteomics and Metabolomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000372",
    "api_endpoint_template": "/v1/metrics/BEMO:2000372/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000372_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 379,
    "source_record_hash": "770bd2fa8c1eedf14831e8e8caca6d53a1ad4a7b7272433891be0eac41a4e30c",
    "source_references": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 379; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000373",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000373",
    "preferred_label": "Pathway Enrichment Robustness",
    "normalized_label": "pathway_enrichment_robustness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100014",
    "category_label": "Proteomics and Metabolomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100014",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of pathway enrichment robustness.",
    "what_it_measures": "Assesses pathway enrichment robustness using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in pathway enrichment robustness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "related_frameworks_source": "MIAPE; HUPO PSI; Metabolomics Standards",
    "closely_related_metrics_source": "Metabolic Feature Reproducibility; Cross-Omics Concordance",
    "common_misinterpretations": "Treating pathway enrichment robustness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "domain_applicability": "Proteomics and Metabolomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000373",
    "api_endpoint_template": "/v1/metrics/BEMO:2000373/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000373_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 380,
    "source_record_hash": "1a891a794290e0f5eee9ca88b64bc6b46d5840f63c8709e0e546399158fbb914",
    "source_references": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 380; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000374",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000374",
    "preferred_label": "Peptide Identification Confidence",
    "normalized_label": "peptide_identification_confidence",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100014",
    "category_label": "Proteomics and Metabolomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100014",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The justified degree of certainty assigned to peptide identification given the quantity, quality, consistency, and limitations of supporting evidence.",
    "what_it_measures": "Assesses peptide identification confidence using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in peptide identification confidence can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Target-decoy analysis; spectral scoring; reference standards; replicate injections; retention-time and mass-error monitoring; orthogonal confirmation.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "related_frameworks_source": "MIAPE; HUPO PSI; Metabolomics Standards",
    "closely_related_metrics_source": "Protein Identification Confidence; False Discovery Rate Control",
    "common_misinterpretations": "Treating peptide identification confidence as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "domain_applicability": "Proteomics and Metabolomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000374",
    "api_endpoint_template": "/v1/metrics/BEMO:2000374/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000374_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 381,
    "source_record_hash": "7f78eede8aa05781dde3f12d7ea8111e1c0b552f5b722c402b0de5323e65b0ea",
    "source_references": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 381; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000375",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000375",
    "preferred_label": "Peptide-Spectrum Match Quality",
    "normalized_label": "peptide_spectrum_match_quality",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100014",
    "category_label": "Proteomics and Metabolomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100014",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of peptide-spectrum match quality.",
    "what_it_measures": "Assesses peptide-spectrum match quality using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in peptide-spectrum match quality can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Target-decoy analysis; spectral scoring; reference standards; replicate injections; retention-time and mass-error monitoring; orthogonal confirmation.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "related_frameworks_source": "MIAPE; HUPO PSI; Metabolomics Standards",
    "closely_related_metrics_source": "False Discovery Rate Control; Protein Inference Reliability; Proteome Coverage",
    "common_misinterpretations": "Treating peptide-spectrum match quality as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "domain_applicability": "Proteomics and Metabolomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000375",
    "api_endpoint_template": "/v1/metrics/BEMO:2000375/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000375_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 382,
    "source_record_hash": "69f7898b8265a7daaa45bd90d4d5387c92da6521721d3c4901a5c208a63f0169",
    "source_references": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 382; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000376",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000376",
    "preferred_label": "Post-Translational Modification Localization Confidence",
    "normalized_label": "post_translational_modification_localization_confidence",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100014",
    "category_label": "Proteomics and Metabolomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100014",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The justified degree of certainty assigned to post-translational modification localization given the quantity, quality, consistency, and limitations of supporting evidence.",
    "what_it_measures": "Assesses post-translational modification localization confidence using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in post-translational modification localization confidence can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "related_frameworks_source": "MIAPE; HUPO PSI; Metabolomics Standards",
    "closely_related_metrics_source": "Fragmentation Spectrum Quality; Proteoform Identification Confidence; Metabolite Identification Confidence",
    "common_misinterpretations": "Treating post-translational modification localization confidence as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "domain_applicability": "Proteomics and Metabolomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000376",
    "api_endpoint_template": "/v1/metrics/BEMO:2000376/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000376_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 383,
    "source_record_hash": "6761ab89a934b85357a2d58a5e53503065037a8cd658104babdb5536291a3653",
    "source_references": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 383; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000377",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000377",
    "preferred_label": "Protein Identification Confidence",
    "normalized_label": "protein_identification_confidence",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100014",
    "category_label": "Proteomics and Metabolomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100014",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The justified degree of certainty assigned to protein identification given the quantity, quality, consistency, and limitations of supporting evidence.",
    "what_it_measures": "Assesses protein identification confidence using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in protein identification confidence can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Target-decoy analysis; spectral scoring; reference standards; replicate injections; retention-time and mass-error monitoring; orthogonal confirmation.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "related_frameworks_source": "MIAPE; HUPO PSI; Metabolomics Standards",
    "closely_related_metrics_source": "Peptide Identification Confidence; False Discovery Rate Control; Peptide-Spectrum Match Quality",
    "common_misinterpretations": "Treating protein identification confidence as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "domain_applicability": "Proteomics and Metabolomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000377",
    "api_endpoint_template": "/v1/metrics/BEMO:2000377/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000377_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 384,
    "source_record_hash": "86cf8ad175ebd274f625e908935f946750c2c41a33f40e7a8dc33224d8db7d28",
    "source_references": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 384; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000378",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000378",
    "preferred_label": "Protein Inference Reliability",
    "normalized_label": "protein_inference_reliability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100014",
    "category_label": "Proteomics and Metabolomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100014",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of protein inference reliability.",
    "what_it_measures": "Assesses protein inference reliability using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in protein inference reliability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Target-decoy analysis; spectral scoring; reference standards; replicate injections; retention-time and mass-error monitoring; orthogonal confirmation.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "related_frameworks_source": "MIAPE; HUPO PSI; Metabolomics Standards",
    "closely_related_metrics_source": "Peptide-Spectrum Match Quality; Proteome Coverage; Sequence Coverage",
    "common_misinterpretations": "Treating protein inference reliability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "domain_applicability": "Proteomics and Metabolomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000378",
    "api_endpoint_template": "/v1/metrics/BEMO:2000378/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000378_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 385,
    "source_record_hash": "601ad0978c475da6065d2502b00169f5521ae97cb0543ad15ad88f49903cb27e",
    "source_references": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 385; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000379",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000379",
    "preferred_label": "Proteoform Identification Confidence",
    "normalized_label": "proteoform_identification_confidence",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100014",
    "category_label": "Proteomics and Metabolomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100014",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The justified degree of certainty assigned to proteoform identification given the quantity, quality, consistency, and limitations of supporting evidence.",
    "what_it_measures": "Assesses proteoform identification confidence using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in proteoform identification confidence can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "related_frameworks_source": "MIAPE; HUPO PSI; Metabolomics Standards",
    "closely_related_metrics_source": "Post-Translational Modification Localization Confidence; Metabolite Identification Confidence; Metabolite Annotation Level",
    "common_misinterpretations": "Treating proteoform identification confidence as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "domain_applicability": "Proteomics and Metabolomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000379",
    "api_endpoint_template": "/v1/metrics/BEMO:2000379/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000379_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 386,
    "source_record_hash": "8df86e86625f432ba76b927808300a9cfa4a9b6844cae40ca0c6240f4f899eda",
    "source_references": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 386; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000380",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000380",
    "preferred_label": "Proteome Coverage",
    "normalized_label": "proteome_coverage",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100014",
    "category_label": "Proteomics and Metabolomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100014",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The proportion and representativeness of the relevant proteome captured by the evidence or measurement process.",
    "what_it_measures": "Assesses proteome coverage using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in proteome coverage can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "related_frameworks_source": "MIAPE; HUPO PSI; Metabolomics Standards",
    "closely_related_metrics_source": "Protein Inference Reliability; Sequence Coverage; Quantification Precision",
    "common_misinterpretations": "Treating proteome coverage as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "domain_applicability": "Proteomics and Metabolomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000380",
    "api_endpoint_template": "/v1/metrics/BEMO:2000380/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000380_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 387,
    "source_record_hash": "5fec1390446b523e8b6072b1babcb11902375d326650ad448b800e258e0a8401",
    "source_references": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 387; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000381",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000381",
    "preferred_label": "Quantification Accuracy",
    "normalized_label": "quantification_accuracy",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100014",
    "category_label": "Proteomics and Metabolomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100014",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The closeness of quantification to the accepted reference or true value.",
    "what_it_measures": "Assesses quantification accuracy using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in quantification accuracy can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "related_frameworks_source": "MIAPE; HUPO PSI; Metabolomics Standards",
    "closely_related_metrics_source": "Quantification Precision; Dynamic Range Coverage; Missing-Value Burden",
    "common_misinterpretations": "Treating quantification accuracy as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "domain_applicability": "Proteomics and Metabolomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000381",
    "api_endpoint_template": "/v1/metrics/BEMO:2000381/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000381_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 388,
    "source_record_hash": "5205abd1da59c18e5b7272ce8586c2ec2bee590ad36aa3289ce71f4aa4c17c0b",
    "source_references": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 388; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000382",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000382",
    "preferred_label": "Quantification Precision",
    "normalized_label": "quantification_precision",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100014",
    "category_label": "Proteomics and Metabolomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100014",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The closeness of repeated estimates or measurements and the narrowness of uncertainty around quantification.",
    "what_it_measures": "Assesses quantification precision using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in quantification precision can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "related_frameworks_source": "MIAPE; HUPO PSI; Metabolomics Standards",
    "closely_related_metrics_source": "Sequence Coverage; Quantification Accuracy; Dynamic Range Coverage",
    "common_misinterpretations": "Treating quantification precision as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "domain_applicability": "Proteomics and Metabolomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000382",
    "api_endpoint_template": "/v1/metrics/BEMO:2000382/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000382_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 389,
    "source_record_hash": "6e5af7c1fffa7603da0abd7518a670fd09cade5fe3e47c8417886f91e6b4e07a",
    "source_references": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 389; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000383",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000383",
    "preferred_label": "Retention-Time Stability",
    "normalized_label": "retention_time_stability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100014",
    "category_label": "Proteomics and Metabolomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100014",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of retention-time stability.",
    "what_it_measures": "Assesses retention-time stability using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in retention-time stability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Target-decoy analysis; spectral scoring; reference standards; replicate injections; retention-time and mass-error monitoring; orthogonal confirmation.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "related_frameworks_source": "MIAPE; HUPO PSI; Metabolomics Standards",
    "closely_related_metrics_source": "Ion Suppression Assessment; Mass Accuracy; Isotope Pattern Fidelity",
    "common_misinterpretations": "Treating retention-time stability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "domain_applicability": "Proteomics and Metabolomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000383",
    "api_endpoint_template": "/v1/metrics/BEMO:2000383/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000383_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 390,
    "source_record_hash": "7ed489b83705dc957b891fd6483e7b54ca4c70547f903f7dfa9e53d0ca59fa58",
    "source_references": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 390; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000384",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000384",
    "preferred_label": "Sequence Coverage",
    "normalized_label": "sequence_coverage",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100014",
    "category_label": "Proteomics and Metabolomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100014",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The proportion and representativeness of the relevant sequence captured by the evidence or measurement process.",
    "what_it_measures": "Assesses sequence coverage using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in sequence coverage can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "related_frameworks_source": "MIAPE; HUPO PSI; Metabolomics Standards",
    "closely_related_metrics_source": "Proteome Coverage; Quantification Precision; Quantification Accuracy",
    "common_misinterpretations": "Treating sequence coverage as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "domain_applicability": "Proteomics and Metabolomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000384",
    "api_endpoint_template": "/v1/metrics/BEMO:2000384/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000384_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 391,
    "source_record_hash": "f98e41911ad517a10150d0d24373bec15a553a9812e119c2e6a10081e9a89aaf",
    "source_references": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 391; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000385",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000385",
    "preferred_label": "Spectral Library Match Quality",
    "normalized_label": "spectral_library_match_quality",
    "abbreviation": "",
    "pillar_id": "BEMO:1000007",
    "pillar_label": "Genetics, Omics, and Systems Biology",
    "category_id": "BEMO:1100014",
    "category_label": "Proteomics and Metabolomics",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100014",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of spectral library match quality.",
    "what_it_measures": "Assesses spectral library match quality using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in spectral library match quality can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "related_frameworks_source": "MIAPE; HUPO PSI; Metabolomics Standards",
    "closely_related_metrics_source": "Metabolite Annotation Level; Internal Standard Performance; Extraction Recovery",
    "common_misinterpretations": "Treating spectral library match quality as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies",
    "domain_applicability": "Proteomics and Metabolomics",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000385",
    "api_endpoint_template": "/v1/metrics/BEMO:2000385/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000385_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 392,
    "source_record_hash": "5f1fa5732761f5ddf9eae216997fca90d2ec95264368ca476160849aac179e9a",
    "source_references": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 392; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/",
    "obo_subset": "bemo_genetics_omics_and_systems_biology",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000386",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000386",
    "preferred_label": "Analytical Reproducibility",
    "normalized_label": "analytical_reproducibility",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100015",
    "category_label": "Reproducibility and Replication",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100015",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which analytical reproducibility yields concordant results under the specified repeated-analysis or repeated-measurement conditions.",
    "what_it_measures": "Assesses analytical reproducibility using evidence appropriate to reproducibility and replication, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in analytical reproducibility can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All experimental, computational, clinical, and omics studies",
    "related_frameworks_source": "PRISMA; CONSORT; MIAME; MINSEQE; MIAPE; ARRIVE 2.0",
    "closely_related_metrics_source": "Conceptual Replication Success; Computational Reproducibility; Experimental Reproducibility",
    "common_misinterpretations": "Treating analytical reproducibility as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All experimental, computational, clinical, and omics studies",
    "domain_applicability": "Reproducibility and Replication",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000386",
    "api_endpoint_template": "/v1/metrics/BEMO:2000386/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000386_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 393,
    "source_record_hash": "8e400bbae5ea25bca3af45f9c956cb2ceeb52ded61247de3b92d5364736bab99",
    "source_references": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 393; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000387",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000387",
    "preferred_label": "Code Availability",
    "normalized_label": "code_availability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100015",
    "category_label": "Reproducibility and Replication",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100015",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of code availability.",
    "what_it_measures": "Assesses code availability using evidence appropriate to reproducibility and replication, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in code availability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All experimental, computational, clinical, and omics studies",
    "related_frameworks_source": "PRISMA; CONSORT; MIAME; MINSEQE; MIAPE; ARRIVE 2.0",
    "closely_related_metrics_source": "Material Availability; Data Availability; Random-Seed Stability",
    "common_misinterpretations": "Treating code availability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All experimental, computational, clinical, and omics studies",
    "domain_applicability": "Reproducibility and Replication",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000387",
    "api_endpoint_template": "/v1/metrics/BEMO:2000387/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000387_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 394,
    "source_record_hash": "196f2dc58cfb1ea70e003d9904020fcfd1f4feec7308ace2e85d573eb71d3b5e",
    "source_references": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 394; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000388",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000388",
    "preferred_label": "Computational Reproducibility",
    "normalized_label": "computational_reproducibility",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100015",
    "category_label": "Reproducibility and Replication",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100015",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which computational reproducibility yields concordant results under the specified repeated-analysis or repeated-measurement conditions.",
    "what_it_measures": "Assesses computational reproducibility using evidence appropriate to reproducibility and replication, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in computational reproducibility can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All experimental, computational, clinical, and omics studies",
    "related_frameworks_source": "PRISMA; CONSORT; MIAME; MINSEQE; MIAPE; ARRIVE 2.0",
    "closely_related_metrics_source": "Analytical Reproducibility; Experimental Reproducibility; Interlaboratory Reproducibility",
    "common_misinterpretations": "Treating computational reproducibility as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All experimental, computational, clinical, and omics studies",
    "domain_applicability": "Reproducibility and Replication",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000388",
    "api_endpoint_template": "/v1/metrics/BEMO:2000388/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000388_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 395,
    "source_record_hash": "c15f070192e578e50deb91384b3e8099e5c4b1a0c28cc84d1ac6a3163d36cd17",
    "source_references": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 395; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000389",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000389",
    "preferred_label": "Conceptual Replication Success",
    "normalized_label": "conceptual_replication_success",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100015",
    "category_label": "Reproducibility and Replication",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100015",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of conceptual replication success.",
    "what_it_measures": "Assesses conceptual replication success using evidence appropriate to reproducibility and replication, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in conceptual replication success can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All experimental, computational, clinical, and omics studies",
    "related_frameworks_source": "PRISMA; CONSORT; MIAME; MINSEQE; MIAPE; ARRIVE 2.0",
    "closely_related_metrics_source": "Direct Replication Success; Analytical Reproducibility; Computational Reproducibility",
    "common_misinterpretations": "Treating conceptual replication success as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All experimental, computational, clinical, and omics studies",
    "domain_applicability": "Reproducibility and Replication",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000389",
    "api_endpoint_template": "/v1/metrics/BEMO:2000389/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000389_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 396,
    "source_record_hash": "45fcdc0cd9da1d73796f886d24683b4f40ead7f7a14a06e84d39631b66a910ad",
    "source_references": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 396; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000390",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000390",
    "preferred_label": "Data Availability",
    "normalized_label": "data_availability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100015",
    "category_label": "Reproducibility and Replication",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100015",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of data availability.",
    "what_it_measures": "Assesses data availability using evidence appropriate to reproducibility and replication, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in data availability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All experimental, computational, clinical, and omics studies",
    "related_frameworks_source": "PRISMA; CONSORT; MIAME; MINSEQE; MIAPE; ARRIVE 2.0",
    "closely_related_metrics_source": "Code Availability; Random-Seed Stability; Researcher-Degrees-of-Freedom Sensitivity",
    "common_misinterpretations": "Treating data availability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All experimental, computational, clinical, and omics studies",
    "domain_applicability": "Reproducibility and Replication",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000390",
    "api_endpoint_template": "/v1/metrics/BEMO:2000390/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000390_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 397,
    "source_record_hash": "89d3d59a31fe591c17a3c61f83a55d18326e4b311b8033047e95bfb2a93715fa",
    "source_references": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 397; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000391",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000391",
    "preferred_label": "Data Provenance Completeness",
    "normalized_label": "data_provenance_completeness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100015",
    "category_label": "Reproducibility and Replication",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100015",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which all scientifically necessary components of data provenance are present, documented, and evaluable.",
    "what_it_measures": "Assesses data provenance completeness using evidence appropriate to reproducibility and replication, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in data provenance completeness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All experimental, computational, clinical, and omics studies",
    "related_frameworks_source": "PRISMA; CONSORT; MIAME; MINSEQE; MIAPE; ARRIVE 2.0",
    "closely_related_metrics_source": "Reanalysis Concordance; Protocol Reproducibility; Material Availability",
    "common_misinterpretations": "Treating data provenance completeness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All experimental, computational, clinical, and omics studies",
    "domain_applicability": "Reproducibility and Replication",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000391",
    "api_endpoint_template": "/v1/metrics/BEMO:2000391/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000391_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 398,
    "source_record_hash": "da25c768c2ee710f0cf6b50b686a1880c8166dd651b4f062c14e952fc1bdf622",
    "source_references": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 398; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000392",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000392",
    "preferred_label": "Direct Replication Success",
    "normalized_label": "direct_replication_success",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100015",
    "category_label": "Reproducibility and Replication",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100015",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of direct replication success.",
    "what_it_measures": "Assesses direct replication success using evidence appropriate to reproducibility and replication, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in direct replication success can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All experimental, computational, clinical, and omics studies",
    "related_frameworks_source": "PRISMA; CONSORT; MIAME; MINSEQE; MIAPE; ARRIVE 2.0",
    "closely_related_metrics_source": "Independent Replication Strength; Conceptual Replication Success; Analytical Reproducibility",
    "common_misinterpretations": "Treating direct replication success as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All experimental, computational, clinical, and omics studies",
    "domain_applicability": "Reproducibility and Replication",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000392",
    "api_endpoint_template": "/v1/metrics/BEMO:2000392/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000392_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 399,
    "source_record_hash": "e6b0ec1b803bb2c7cb8becab175dbb88ab91c9d8ccd3f713a814c836846ea547",
    "source_references": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 399; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000393",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000393",
    "preferred_label": "Experimental Reproducibility",
    "normalized_label": "experimental_reproducibility",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100015",
    "category_label": "Reproducibility and Replication",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100015",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which experimental reproducibility yields concordant results under the specified repeated-analysis or repeated-measurement conditions.",
    "what_it_measures": "Assesses experimental reproducibility using evidence appropriate to reproducibility and replication, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in experimental reproducibility can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All experimental, computational, clinical, and omics studies",
    "related_frameworks_source": "PRISMA; CONSORT; MIAME; MINSEQE; MIAPE; ARRIVE 2.0",
    "closely_related_metrics_source": "Computational Reproducibility; Interlaboratory Reproducibility; Intralaboratory Repeatability",
    "common_misinterpretations": "Treating experimental reproducibility as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All experimental, computational, clinical, and omics studies",
    "domain_applicability": "Reproducibility and Replication",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000393",
    "api_endpoint_template": "/v1/metrics/BEMO:2000393/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000393_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 400,
    "source_record_hash": "6c9d1f649c85d73c0009300283cb79e817b0ca9b1d53444f1a4aa4b5a2e6d8ae",
    "source_references": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 400; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000394",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000394",
    "preferred_label": "Independent Replication Strength",
    "normalized_label": "independent_replication_strength",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100015",
    "category_label": "Reproducibility and Replication",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100015",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting independent replication.",
    "what_it_measures": "Assesses independent replication strength using evidence appropriate to reproducibility and replication, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in independent replication strength can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All experimental, computational, clinical, and omics studies",
    "related_frameworks_source": "PRISMA; CONSORT; MIAME; MINSEQE; MIAPE; ARRIVE 2.0",
    "closely_related_metrics_source": "Direct Replication Success; Conceptual Replication Success",
    "common_misinterpretations": "Treating independent replication strength as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All experimental, computational, clinical, and omics studies",
    "domain_applicability": "Reproducibility and Replication",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000394",
    "api_endpoint_template": "/v1/metrics/BEMO:2000394/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000394_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 401,
    "source_record_hash": "3837461a84fca58515b90e02475b1cf195c845c2cf4704aa9d0c7c2b412d9406",
    "source_references": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 401; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000395",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000395",
    "preferred_label": "Inferential Reproducibility",
    "normalized_label": "inferential_reproducibility",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100015",
    "category_label": "Reproducibility and Replication",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100015",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which inferential reproducibility yields concordant results under the specified repeated-analysis or repeated-measurement conditions.",
    "what_it_measures": "Assesses inferential reproducibility using evidence appropriate to reproducibility and replication, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in inferential reproducibility can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All experimental, computational, clinical, and omics studies",
    "related_frameworks_source": "PRISMA; CONSORT; MIAME; MINSEQE; MIAPE; ARRIVE 2.0",
    "closely_related_metrics_source": "Result Reproducibility; Reanalysis Concordance; Data Provenance Completeness",
    "common_misinterpretations": "Treating inferential reproducibility as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All experimental, computational, clinical, and omics studies",
    "domain_applicability": "Reproducibility and Replication",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000395",
    "api_endpoint_template": "/v1/metrics/BEMO:2000395/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000395_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 402,
    "source_record_hash": "b49eb32e7bf118727039f0240b17aee8970c665e4a359a2bcecc87341188ecf1",
    "source_references": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 402; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000396",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000396",
    "preferred_label": "Interlaboratory Reproducibility",
    "normalized_label": "interlaboratory_reproducibility",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100015",
    "category_label": "Reproducibility and Replication",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100015",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which interlaboratory reproducibility yields concordant results under the specified repeated-analysis or repeated-measurement conditions.",
    "what_it_measures": "Assesses interlaboratory reproducibility using evidence appropriate to reproducibility and replication, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in interlaboratory reproducibility can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All experimental, computational, clinical, and omics studies",
    "related_frameworks_source": "PRISMA; CONSORT; MIAME; MINSEQE; MIAPE; ARRIVE 2.0",
    "closely_related_metrics_source": "Experimental Reproducibility; Intralaboratory Repeatability; Method Reproducibility",
    "common_misinterpretations": "Treating interlaboratory reproducibility as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All experimental, computational, clinical, and omics studies",
    "domain_applicability": "Reproducibility and Replication",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000396",
    "api_endpoint_template": "/v1/metrics/BEMO:2000396/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000396_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 403,
    "source_record_hash": "0977ae8d7278730723c8d024585a95d1125aa9fe6da897fe977a079b172ddb48",
    "source_references": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 403; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000397",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000397",
    "preferred_label": "Intralaboratory Repeatability",
    "normalized_label": "intralaboratory_repeatability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100015",
    "category_label": "Reproducibility and Replication",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100015",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which intralaboratory repeatability yields concordant results under the specified repeated-analysis or repeated-measurement conditions.",
    "what_it_measures": "Assesses intralaboratory repeatability using evidence appropriate to reproducibility and replication, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in intralaboratory repeatability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All experimental, computational, clinical, and omics studies",
    "related_frameworks_source": "PRISMA; CONSORT; MIAME; MINSEQE; MIAPE; ARRIVE 2.0",
    "closely_related_metrics_source": "Interlaboratory Reproducibility; Method Reproducibility; Result Reproducibility",
    "common_misinterpretations": "Treating intralaboratory repeatability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All experimental, computational, clinical, and omics studies",
    "domain_applicability": "Reproducibility and Replication",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000397",
    "api_endpoint_template": "/v1/metrics/BEMO:2000397/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000397_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 404,
    "source_record_hash": "44bfb4ae3b82bb963a97cc8f3dfed3bd610b7903405993c8f3031931f746d1ce",
    "source_references": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 404; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000398",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000398",
    "preferred_label": "Material Availability",
    "normalized_label": "material_availability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100015",
    "category_label": "Reproducibility and Replication",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100015",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of material availability.",
    "what_it_measures": "Assesses material availability using evidence appropriate to reproducibility and replication, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in material availability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All experimental, computational, clinical, and omics studies",
    "related_frameworks_source": "PRISMA; CONSORT; MIAME; MINSEQE; MIAPE; ARRIVE 2.0",
    "closely_related_metrics_source": "Protocol Reproducibility; Code Availability; Data Availability",
    "common_misinterpretations": "Treating material availability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All experimental, computational, clinical, and omics studies",
    "domain_applicability": "Reproducibility and Replication",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000398",
    "api_endpoint_template": "/v1/metrics/BEMO:2000398/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000398_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 405,
    "source_record_hash": "ad24de4b8dd0c9ae8c1a3d7d5fcdd166b9bd923967cbf8032882e26fce35feb2",
    "source_references": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 405; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000399",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000399",
    "preferred_label": "Method Reproducibility",
    "normalized_label": "method_reproducibility",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100015",
    "category_label": "Reproducibility and Replication",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100015",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which method reproducibility yields concordant results under the specified repeated-analysis or repeated-measurement conditions.",
    "what_it_measures": "Assesses method reproducibility using evidence appropriate to reproducibility and replication, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in method reproducibility can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All experimental, computational, clinical, and omics studies",
    "related_frameworks_source": "PRISMA; CONSORT; MIAME; MINSEQE; MIAPE; ARRIVE 2.0",
    "closely_related_metrics_source": "Intralaboratory Repeatability; Result Reproducibility; Inferential Reproducibility",
    "common_misinterpretations": "Treating method reproducibility as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All experimental, computational, clinical, and omics studies",
    "domain_applicability": "Reproducibility and Replication",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000399",
    "api_endpoint_template": "/v1/metrics/BEMO:2000399/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000399_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 406,
    "source_record_hash": "b36c4ba0356ae6813b5bb255ebc6934635b0cbf83c44326cfea7019592803c5e",
    "source_references": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 406; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000400",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000400",
    "preferred_label": "Multiverse Analysis Robustness",
    "normalized_label": "multiverse_analysis_robustness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100015",
    "category_label": "Reproducibility and Replication",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100015",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of multiverse analysis robustness.",
    "what_it_measures": "Assesses multiverse analysis robustness using evidence appropriate to reproducibility and replication, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in multiverse analysis robustness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All experimental, computational, clinical, and omics studies",
    "related_frameworks_source": "PRISMA; CONSORT; MIAME; MINSEQE; MIAPE; ARRIVE 2.0",
    "closely_related_metrics_source": "Researcher-Degrees-of-Freedom Sensitivity; Specification-Curve Robustness",
    "common_misinterpretations": "Treating multiverse analysis robustness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Specialized / infrequent",
    "maturity_of_metric": "Developing",
    "references_source": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Developing; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All experimental, computational, clinical, and omics studies",
    "domain_applicability": "Reproducibility and Replication",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000400",
    "api_endpoint_template": "/v1/metrics/BEMO:2000400/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000400_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 407,
    "source_record_hash": "80472d064c943a6566bee4bd605245ecac370ebde0eb5ae577d7687482d47cc8",
    "source_references": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 407; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000401",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000401",
    "preferred_label": "Protocol Reproducibility",
    "normalized_label": "protocol_reproducibility",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100015",
    "category_label": "Reproducibility and Replication",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100015",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which protocol reproducibility yields concordant results under the specified repeated-analysis or repeated-measurement conditions.",
    "what_it_measures": "Assesses protocol reproducibility using evidence appropriate to reproducibility and replication, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in protocol reproducibility can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All experimental, computational, clinical, and omics studies",
    "related_frameworks_source": "PRISMA; CONSORT; MIAME; MINSEQE; MIAPE; ARRIVE 2.0",
    "closely_related_metrics_source": "Data Provenance Completeness; Material Availability; Code Availability",
    "common_misinterpretations": "Treating protocol reproducibility as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All experimental, computational, clinical, and omics studies",
    "domain_applicability": "Reproducibility and Replication",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000401",
    "api_endpoint_template": "/v1/metrics/BEMO:2000401/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000401_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 408,
    "source_record_hash": "caa28491bc96ceb6cd2e1c6685b9eb89f21391a6d4502473143986af13cc088b",
    "source_references": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 408; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000402",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000402",
    "preferred_label": "Random-Seed Stability",
    "normalized_label": "random_seed_stability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100015",
    "category_label": "Reproducibility and Replication",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100015",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of random-seed stability.",
    "what_it_measures": "Assesses random-seed stability using evidence appropriate to reproducibility and replication, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in random-seed stability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All experimental, computational, clinical, and omics studies",
    "related_frameworks_source": "PRISMA; CONSORT; MIAME; MINSEQE; MIAPE; ARRIVE 2.0",
    "closely_related_metrics_source": "Data Availability; Researcher-Degrees-of-Freedom Sensitivity; Multiverse Analysis Robustness",
    "common_misinterpretations": "Treating random-seed stability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All experimental, computational, clinical, and omics studies",
    "domain_applicability": "Reproducibility and Replication",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000402",
    "api_endpoint_template": "/v1/metrics/BEMO:2000402/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000402_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 409,
    "source_record_hash": "c1a5a2e956afa3ff1606fb1893282ee7b8d5d3733fbd04798630fe0746f86074",
    "source_references": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 409; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000403",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000403",
    "preferred_label": "Reanalysis Concordance",
    "normalized_label": "reanalysis_concordance",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100015",
    "category_label": "Reproducibility and Replication",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100015",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree of agreement in reanalysis across measurements, studies, methods, populations, or biological levels.",
    "what_it_measures": "Assesses reanalysis concordance using evidence appropriate to reproducibility and replication, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in reanalysis concordance can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All experimental, computational, clinical, and omics studies",
    "related_frameworks_source": "PRISMA; CONSORT; MIAME; MINSEQE; MIAPE; ARRIVE 2.0",
    "closely_related_metrics_source": "Inferential Reproducibility; Data Provenance Completeness; Protocol Reproducibility",
    "common_misinterpretations": "Treating reanalysis concordance as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All experimental, computational, clinical, and omics studies",
    "domain_applicability": "Reproducibility and Replication",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000403",
    "api_endpoint_template": "/v1/metrics/BEMO:2000403/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000403_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 410,
    "source_record_hash": "07f0b47b85e307e7887d3c938a89cbcad651d37d8bfa888ea4ce710d25410a29",
    "source_references": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 410; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000404",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000404",
    "preferred_label": "Researcher-Degrees-of-Freedom Sensitivity",
    "normalized_label": "researcher_degrees_of_freedom_sensitivity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100015",
    "category_label": "Reproducibility and Replication",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100015",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of researcher-degrees-of-freedom sensitivity.",
    "what_it_measures": "Assesses researcher-degrees-of-freedom sensitivity using evidence appropriate to reproducibility and replication, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in researcher-degrees-of-freedom sensitivity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified threshold; valid reference standard; complete 2×2 classification; confidence intervals; spectrum and prevalence assessment.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All experimental, computational, clinical, and omics studies",
    "related_frameworks_source": "PRISMA; CONSORT; MIAME; MINSEQE; MIAPE; ARRIVE 2.0",
    "closely_related_metrics_source": "Random-Seed Stability; Multiverse Analysis Robustness; Specification-Curve Robustness",
    "common_misinterpretations": "Treating researcher-degrees-of-freedom sensitivity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All experimental, computational, clinical, and omics studies",
    "domain_applicability": "Reproducibility and Replication",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000404",
    "api_endpoint_template": "/v1/metrics/BEMO:2000404/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000404_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 411,
    "source_record_hash": "c196ee0e5b3c49cffc78d559a15b400e1dec74f4854200e7fbd341eef60a59c4",
    "source_references": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 411; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000405",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000405",
    "preferred_label": "Result Reproducibility",
    "normalized_label": "result_reproducibility",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100015",
    "category_label": "Reproducibility and Replication",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100015",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which result reproducibility yields concordant results under the specified repeated-analysis or repeated-measurement conditions.",
    "what_it_measures": "Assesses result reproducibility using evidence appropriate to reproducibility and replication, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in result reproducibility can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All experimental, computational, clinical, and omics studies",
    "related_frameworks_source": "PRISMA; CONSORT; MIAME; MINSEQE; MIAPE; ARRIVE 2.0",
    "closely_related_metrics_source": "Method Reproducibility; Inferential Reproducibility; Reanalysis Concordance",
    "common_misinterpretations": "Treating result reproducibility as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All experimental, computational, clinical, and omics studies",
    "domain_applicability": "Reproducibility and Replication",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000405",
    "api_endpoint_template": "/v1/metrics/BEMO:2000405/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000405_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 412,
    "source_record_hash": "60121a2998efa943018d3ff7dd4130d4332ee279da0e8111b650ea175e9dacce",
    "source_references": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 412; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000406",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000406",
    "preferred_label": "Specification-Curve Robustness",
    "normalized_label": "specification_curve_robustness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100015",
    "category_label": "Reproducibility and Replication",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100015",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of specification-curve robustness.",
    "what_it_measures": "Assesses specification-curve robustness using evidence appropriate to reproducibility and replication, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in specification-curve robustness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All experimental, computational, clinical, and omics studies",
    "related_frameworks_source": "PRISMA; CONSORT; MIAME; MINSEQE; MIAPE; ARRIVE 2.0",
    "closely_related_metrics_source": "Multiverse Analysis Robustness",
    "common_misinterpretations": "Treating specification-curve robustness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Specialized / infrequent",
    "maturity_of_metric": "Developing",
    "references_source": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Developing; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All experimental, computational, clinical, and omics studies",
    "domain_applicability": "Reproducibility and Replication",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000406",
    "api_endpoint_template": "/v1/metrics/BEMO:2000406/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000406_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 413,
    "source_record_hash": "290b2551a20c17c23c05ae84270ce7ac2c9d4a43b9817050cdbe8a353ce743ac",
    "source_references": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 413; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.fged.org/projects/miame | https://www.fged.org/projects/minseqe/ | https://www.psidev.info/miape | https://arriveguidelines.org/arrive-guidelines",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000407",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000407",
    "preferred_label": "Code-Sharing Transparency",
    "normalized_label": "code_sharing_transparency",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100016",
    "category_label": "Research Transparency and Reporting Completeness",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100016",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of code-sharing transparency.",
    "what_it_measures": "Assesses code-sharing transparency using evidence appropriate to research transparency and reporting completeness, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in code-sharing transparency can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Study report / dataset / evidence package",
    "applicable_study_types_source": "All biomedical study reports and data releases",
    "related_frameworks_source": "EQUATOR; PRISMA; CONSORT; STROBE; STARD; TRIPOD; CARE; CHEERS",
    "closely_related_metrics_source": "Data-Sharing Transparency; Materials-and-Reagents Reporting Completeness; Metadata Completeness",
    "common_misinterpretations": "Treating code-sharing transparency as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Study report / dataset / evidence package",
    "study_type_applicability": "All biomedical study reports and data releases",
    "domain_applicability": "Research Transparency and Reporting Completeness",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000407",
    "api_endpoint_template": "/v1/metrics/BEMO:2000407/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000407_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 414,
    "source_record_hash": "d85d4b116984de9e36c9410fc248aae4b536153c50f4651cf7e48c6b558b49eb",
    "source_references": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 414; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000408",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000408",
    "preferred_label": "Comparator Description Completeness",
    "normalized_label": "comparator_description_completeness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100016",
    "category_label": "Research Transparency and Reporting Completeness",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100016",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which all scientifically necessary components of comparator description are present, documented, and evaluable.",
    "what_it_measures": "Assesses comparator description completeness using evidence appropriate to research transparency and reporting completeness, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in comparator description completeness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Study report / dataset / evidence package",
    "applicable_study_types_source": "All biomedical study reports and data releases",
    "related_frameworks_source": "EQUATOR; PRISMA; CONSORT; STROBE; STARD; TRIPOD; CARE; CHEERS",
    "closely_related_metrics_source": "Intervention Description Completeness; Eligibility Criteria Completeness; Recruitment Reporting Completeness",
    "common_misinterpretations": "Treating comparator description completeness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Study report / dataset / evidence package",
    "study_type_applicability": "All biomedical study reports and data releases",
    "domain_applicability": "Research Transparency and Reporting Completeness",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000408",
    "api_endpoint_template": "/v1/metrics/BEMO:2000408/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000408_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 415,
    "source_record_hash": "a4617b71362b91773383e09e14a13eab2a1f342da234aa0f9bf7cc4400a6ff10",
    "source_references": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 415; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000409",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000409",
    "preferred_label": "Conflict-of-Interest Transparency",
    "normalized_label": "conflict_of_interest_transparency",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100016",
    "category_label": "Research Transparency and Reporting Completeness",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100016",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of conflict-of-interest transparency.",
    "what_it_measures": "Assesses conflict-of-interest transparency using evidence appropriate to research transparency and reporting completeness, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in conflict-of-interest transparency can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Study report / dataset / evidence package",
    "applicable_study_types_source": "All biomedical study reports and data releases",
    "related_frameworks_source": "EQUATOR; PRISMA; CONSORT; STROBE; STARD; TRIPOD; CARE; CHEERS",
    "closely_related_metrics_source": "Funding-Source Transparency; Data-Sharing Transparency; Code-Sharing Transparency",
    "common_misinterpretations": "Treating conflict-of-interest transparency as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Study report / dataset / evidence package",
    "study_type_applicability": "All biomedical study reports and data releases",
    "domain_applicability": "Research Transparency and Reporting Completeness",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000409",
    "api_endpoint_template": "/v1/metrics/BEMO:2000409/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000409_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 416,
    "source_record_hash": "e951e1891736a22e6ef317b85f2f1f3032c69473b10d7ac72b1ed8342656df25",
    "source_references": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 416; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000410",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000410",
    "preferred_label": "Data-Sharing Transparency",
    "normalized_label": "data_sharing_transparency",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100016",
    "category_label": "Research Transparency and Reporting Completeness",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100016",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of data-sharing transparency.",
    "what_it_measures": "Assesses data-sharing transparency using evidence appropriate to research transparency and reporting completeness, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in data-sharing transparency can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Study report / dataset / evidence package",
    "applicable_study_types_source": "All biomedical study reports and data releases",
    "related_frameworks_source": "EQUATOR; PRISMA; CONSORT; STROBE; STARD; TRIPOD; CARE; CHEERS",
    "closely_related_metrics_source": "Conflict-of-Interest Transparency; Code-Sharing Transparency; Materials-and-Reagents Reporting Completeness",
    "common_misinterpretations": "Treating data-sharing transparency as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Study report / dataset / evidence package",
    "study_type_applicability": "All biomedical study reports and data releases",
    "domain_applicability": "Research Transparency and Reporting Completeness",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000410",
    "api_endpoint_template": "/v1/metrics/BEMO:2000410/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000410_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 417,
    "source_record_hash": "24a8774755f1b71359ef7a35f4a7813a446670f2da0ccc38d22836e1a84f1453",
    "source_references": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 417; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000411",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000411",
    "preferred_label": "Deviations-from-Protocol Transparency",
    "normalized_label": "deviations_from_protocol_transparency",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100016",
    "category_label": "Research Transparency and Reporting Completeness",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100016",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of deviations-from-protocol transparency.",
    "what_it_measures": "Assesses deviations-from-protocol transparency using evidence appropriate to research transparency and reporting completeness, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in deviations-from-protocol transparency can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Study report / dataset / evidence package",
    "applicable_study_types_source": "All biomedical study reports and data releases",
    "related_frameworks_source": "EQUATOR; PRISMA; CONSORT; STROBE; STARD; TRIPOD; CARE; CHEERS",
    "closely_related_metrics_source": "Null-Result Interpretability; Reproducibility Information Completeness",
    "common_misinterpretations": "Treating deviations-from-protocol transparency as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Study report / dataset / evidence package",
    "study_type_applicability": "All biomedical study reports and data releases",
    "domain_applicability": "Research Transparency and Reporting Completeness",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000411",
    "api_endpoint_template": "/v1/metrics/BEMO:2000411/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000411_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 418,
    "source_record_hash": "6d08df9b94938aa4356ba3bbe963ef6fed2e0e499e09e30936b635d55a24d3c8",
    "source_references": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 418; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000412",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000412",
    "preferred_label": "Eligibility Criteria Completeness",
    "normalized_label": "eligibility_criteria_completeness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100016",
    "category_label": "Research Transparency and Reporting Completeness",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100016",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which all scientifically necessary components of eligibility criteria are present, documented, and evaluable.",
    "what_it_measures": "Assesses eligibility criteria completeness using evidence appropriate to research transparency and reporting completeness, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in eligibility criteria completeness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Study report / dataset / evidence package",
    "applicable_study_types_source": "All biomedical study reports and data releases",
    "related_frameworks_source": "EQUATOR; PRISMA; CONSORT; STROBE; STARD; TRIPOD; CARE; CHEERS",
    "closely_related_metrics_source": "Comparator Description Completeness; Recruitment Reporting Completeness; Participant Flow Completeness",
    "common_misinterpretations": "Treating eligibility criteria completeness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Study report / dataset / evidence package",
    "study_type_applicability": "All biomedical study reports and data releases",
    "domain_applicability": "Research Transparency and Reporting Completeness",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000412",
    "api_endpoint_template": "/v1/metrics/BEMO:2000412/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000412_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 419,
    "source_record_hash": "02e23f40dd856c6f19f825d6191af4cb70f9ed2e604c47f5cbd7bf406e4d2381",
    "source_references": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 419; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000413",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000413",
    "preferred_label": "Funding-Source Transparency",
    "normalized_label": "funding_source_transparency",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100016",
    "category_label": "Research Transparency and Reporting Completeness",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100016",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of funding-source transparency.",
    "what_it_measures": "Assesses funding-source transparency using evidence appropriate to research transparency and reporting completeness, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in funding-source transparency can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Study report / dataset / evidence package",
    "applicable_study_types_source": "All biomedical study reports and data releases",
    "related_frameworks_source": "EQUATOR; PRISMA; CONSORT; STROBE; STARD; TRIPOD; CARE; CHEERS",
    "closely_related_metrics_source": "Missing-Data Reporting Completeness; Conflict-of-Interest Transparency; Data-Sharing Transparency",
    "common_misinterpretations": "Treating funding-source transparency as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Study report / dataset / evidence package",
    "study_type_applicability": "All biomedical study reports and data releases",
    "domain_applicability": "Research Transparency and Reporting Completeness",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000413",
    "api_endpoint_template": "/v1/metrics/BEMO:2000413/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000413_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 420,
    "source_record_hash": "35377c10ba740cabcf147ce4b6ab00e3a9c4087ca2ca810c337f7fe08223e6f9",
    "source_references": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 420; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000414",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000414",
    "preferred_label": "Harms Reporting Completeness",
    "normalized_label": "harms_reporting_completeness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100016",
    "category_label": "Research Transparency and Reporting Completeness",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100016",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which all scientifically necessary components of harms reporting are present, documented, and evaluable.",
    "what_it_measures": "Assesses harms reporting completeness using evidence appropriate to research transparency and reporting completeness, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in harms reporting completeness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Study report / dataset / evidence package",
    "applicable_study_types_source": "All biomedical study reports and data releases",
    "related_frameworks_source": "EQUATOR; PRISMA; CONSORT; STROBE; STARD; TRIPOD; CARE; CHEERS",
    "closely_related_metrics_source": "Participant Flow Completeness; Statistical Methods Reporting Completeness; Missing-Data Reporting Completeness",
    "common_misinterpretations": "Treating harms reporting completeness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Study report / dataset / evidence package",
    "study_type_applicability": "All biomedical study reports and data releases",
    "domain_applicability": "Research Transparency and Reporting Completeness",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000414",
    "api_endpoint_template": "/v1/metrics/BEMO:2000414/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000414_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 421,
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    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
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    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
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    "xrefs": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
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    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
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    "metric_id": "BEMO:2000415",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000415",
    "preferred_label": "Intervention Description Completeness",
    "normalized_label": "intervention_description_completeness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
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    "category_label": "Research Transparency and Reporting Completeness",
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    "deprecated": false,
    "replacement_id": "",
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    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
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    "why_it_matters": "Material weakness in intervention description completeness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Study report / dataset / evidence package",
    "applicable_study_types_source": "All biomedical study reports and data releases",
    "related_frameworks_source": "EQUATOR; PRISMA; CONSORT; STROBE; STARD; TRIPOD; CARE; CHEERS",
    "closely_related_metrics_source": "Outcome Definition Completeness; Comparator Description Completeness; Eligibility Criteria Completeness",
    "common_misinterpretations": "Treating intervention description completeness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
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    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
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    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Study report / dataset / evidence package",
    "study_type_applicability": "All biomedical study reports and data releases",
    "domain_applicability": "Research Transparency and Reporting Completeness",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000415",
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    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000415_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
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    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 422; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
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    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000416",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000416",
    "preferred_label": "Materials-and-Reagents Reporting Completeness",
    "normalized_label": "materials_and_reagents_reporting_completeness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100016",
    "category_label": "Research Transparency and Reporting Completeness",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100016",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which all scientifically necessary components of materials-and-reagents reporting are present, documented, and evaluable.",
    "what_it_measures": "Assesses materials-and-reagents reporting completeness using evidence appropriate to research transparency and reporting completeness, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in materials-and-reagents reporting completeness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Study report / dataset / evidence package",
    "applicable_study_types_source": "All biomedical study reports and data releases",
    "related_frameworks_source": "EQUATOR; PRISMA; CONSORT; STROBE; STARD; TRIPOD; CARE; CHEERS",
    "closely_related_metrics_source": "Code-Sharing Transparency; Metadata Completeness; Raw-Data Availability",
    "common_misinterpretations": "Treating materials-and-reagents reporting completeness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
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    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
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    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
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    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
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    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Study report / dataset / evidence package",
    "study_type_applicability": "All biomedical study reports and data releases",
    "domain_applicability": "Research Transparency and Reporting Completeness",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000416",
    "api_endpoint_template": "/v1/metrics/BEMO:2000416/compute",
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    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
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    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
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    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
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    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
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    "metric_id": "BEMO:2000417",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000417",
    "preferred_label": "Metadata Completeness",
    "normalized_label": "metadata_completeness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
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    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
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    "why_it_matters": "Material weakness in metadata completeness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
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    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Study report / dataset / evidence package",
    "applicable_study_types_source": "All biomedical study reports and data releases",
    "related_frameworks_source": "EQUATOR; PRISMA; CONSORT; STROBE; STARD; TRIPOD; CARE; CHEERS",
    "closely_related_metrics_source": "Materials-and-Reagents Reporting Completeness; Raw-Data Availability; Processed-Data Availability",
    "common_misinterpretations": "Treating metadata completeness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
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    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
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    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
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    "maximum_value": 1.0,
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    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
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    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
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    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000417",
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    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
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    "source_references": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 424; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000418",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000418",
    "preferred_label": "Missing-Data Reporting Completeness",
    "normalized_label": "missing_data_reporting_completeness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100016",
    "category_label": "Research Transparency and Reporting Completeness",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100016",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which all scientifically necessary components of missing-data reporting are present, documented, and evaluable.",
    "what_it_measures": "Assesses missing-data reporting completeness using evidence appropriate to research transparency and reporting completeness, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in missing-data reporting completeness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Study report / dataset / evidence package",
    "applicable_study_types_source": "All biomedical study reports and data releases",
    "related_frameworks_source": "EQUATOR; PRISMA; CONSORT; STROBE; STARD; TRIPOD; CARE; CHEERS",
    "closely_related_metrics_source": "Statistical Methods Reporting Completeness; Funding-Source Transparency; Conflict-of-Interest Transparency",
    "common_misinterpretations": "Treating missing-data reporting completeness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Study report / dataset / evidence package",
    "study_type_applicability": "All biomedical study reports and data releases",
    "domain_applicability": "Research Transparency and Reporting Completeness",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000418",
    "api_endpoint_template": "/v1/metrics/BEMO:2000418/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000418_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
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    "source_record_hash": "810e02862dfc4630d6f7a0d7bd830ccd305d847e2d0153cfdb863b68f1c2ece8",
    "source_references": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 425; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000419",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000419",
    "preferred_label": "Negative-Result Reporting",
    "normalized_label": "negative_result_reporting",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100016",
    "category_label": "Research Transparency and Reporting Completeness",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100016",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of negative-result reporting.",
    "what_it_measures": "Assesses negative-result reporting using evidence appropriate to research transparency and reporting completeness, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in negative-result reporting can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Study report / dataset / evidence package",
    "applicable_study_types_source": "All biomedical study reports and data releases",
    "related_frameworks_source": "EQUATOR; PRISMA; CONSORT; STROBE; STARD; TRIPOD; CARE; CHEERS",
    "closely_related_metrics_source": "Quality-Control Reporting Completeness; Null-Result Interpretability; Deviations-from-Protocol Transparency",
    "common_misinterpretations": "Treating negative-result reporting as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Study report / dataset / evidence package",
    "study_type_applicability": "All biomedical study reports and data releases",
    "domain_applicability": "Research Transparency and Reporting Completeness",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000419",
    "api_endpoint_template": "/v1/metrics/BEMO:2000419/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000419_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 426,
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    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 426; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
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    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000420",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000420",
    "preferred_label": "Null-Result Interpretability",
    "normalized_label": "null_result_interpretability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100016",
    "category_label": "Research Transparency and Reporting Completeness",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100016",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of null-result interpretability.",
    "what_it_measures": "Assesses null-result interpretability using evidence appropriate to research transparency and reporting completeness, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in null-result interpretability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Study report / dataset / evidence package",
    "applicable_study_types_source": "All biomedical study reports and data releases",
    "related_frameworks_source": "EQUATOR; PRISMA; CONSORT; STROBE; STARD; TRIPOD; CARE; CHEERS",
    "closely_related_metrics_source": "Negative-Result Reporting; Deviations-from-Protocol Transparency; Reproducibility Information Completeness",
    "common_misinterpretations": "Treating null-result interpretability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Study report / dataset / evidence package",
    "study_type_applicability": "All biomedical study reports and data releases",
    "domain_applicability": "Research Transparency and Reporting Completeness",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000420",
    "api_endpoint_template": "/v1/metrics/BEMO:2000420/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000420_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
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    "source_references": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 427; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000421",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000421",
    "preferred_label": "Outcome Definition Completeness",
    "normalized_label": "outcome_definition_completeness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100016",
    "category_label": "Research Transparency and Reporting Completeness",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100016",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which all scientifically necessary components of outcome definition are present, documented, and evaluable.",
    "what_it_measures": "Assesses outcome definition completeness using evidence appropriate to research transparency and reporting completeness, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in outcome definition completeness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Study report / dataset / evidence package",
    "applicable_study_types_source": "All biomedical study reports and data releases",
    "related_frameworks_source": "EQUATOR; PRISMA; CONSORT; STROBE; STARD; TRIPOD; CARE; CHEERS",
    "closely_related_metrics_source": "Prespecified Analysis Adherence; Intervention Description Completeness; Comparator Description Completeness",
    "common_misinterpretations": "Treating outcome definition completeness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Study report / dataset / evidence package",
    "study_type_applicability": "All biomedical study reports and data releases",
    "domain_applicability": "Research Transparency and Reporting Completeness",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000421",
    "api_endpoint_template": "/v1/metrics/BEMO:2000421/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000421_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
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    "source_references": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 428; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000422",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000422",
    "preferred_label": "Participant Flow Completeness",
    "normalized_label": "participant_flow_completeness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100016",
    "category_label": "Research Transparency and Reporting Completeness",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100016",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which all scientifically necessary components of participant flow are present, documented, and evaluable.",
    "what_it_measures": "Assesses participant flow completeness using evidence appropriate to research transparency and reporting completeness, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in participant flow completeness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Study report / dataset / evidence package",
    "applicable_study_types_source": "All biomedical study reports and data releases",
    "related_frameworks_source": "EQUATOR; PRISMA; CONSORT; STROBE; STARD; TRIPOD; CARE; CHEERS",
    "closely_related_metrics_source": "Recruitment Reporting Completeness; Harms Reporting Completeness; Statistical Methods Reporting Completeness",
    "common_misinterpretations": "Treating participant flow completeness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Study report / dataset / evidence package",
    "study_type_applicability": "All biomedical study reports and data releases",
    "domain_applicability": "Research Transparency and Reporting Completeness",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000422",
    "api_endpoint_template": "/v1/metrics/BEMO:2000422/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000422_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
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    "source_references": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 429; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
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    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000423",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000423",
    "preferred_label": "Prespecified Analysis Adherence",
    "normalized_label": "prespecified_analysis_adherence",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100016",
    "category_label": "Research Transparency and Reporting Completeness",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100016",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of prespecified analysis adherence.",
    "what_it_measures": "Assesses prespecified analysis adherence using evidence appropriate to research transparency and reporting completeness, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in prespecified analysis adherence can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Study report / dataset / evidence package",
    "applicable_study_types_source": "All biomedical study reports and data releases",
    "related_frameworks_source": "EQUATOR; PRISMA; CONSORT; STROBE; STARD; TRIPOD; CARE; CHEERS",
    "closely_related_metrics_source": "Prospective Registration; Outcome Definition Completeness; Intervention Description Completeness",
    "common_misinterpretations": "Treating prespecified analysis adherence as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Study report / dataset / evidence package",
    "study_type_applicability": "All biomedical study reports and data releases",
    "domain_applicability": "Research Transparency and Reporting Completeness",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000423",
    "api_endpoint_template": "/v1/metrics/BEMO:2000423/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000423_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
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    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 430; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000424",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000424",
    "preferred_label": "Processed-Data Availability",
    "normalized_label": "processed_data_availability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100016",
    "category_label": "Research Transparency and Reporting Completeness",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100016",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of processed-data availability.",
    "what_it_measures": "Assesses processed-data availability using evidence appropriate to research transparency and reporting completeness, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in processed-data availability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Study report / dataset / evidence package",
    "applicable_study_types_source": "All biomedical study reports and data releases",
    "related_frameworks_source": "EQUATOR; PRISMA; CONSORT; STROBE; STARD; TRIPOD; CARE; CHEERS",
    "closely_related_metrics_source": "Raw-Data Availability; Quality-Control Reporting Completeness; Negative-Result Reporting",
    "common_misinterpretations": "Treating processed-data availability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Study report / dataset / evidence package",
    "study_type_applicability": "All biomedical study reports and data releases",
    "domain_applicability": "Research Transparency and Reporting Completeness",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000424",
    "api_endpoint_template": "/v1/metrics/BEMO:2000424/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000424_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 431,
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    "source_references": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 431; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000425",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000425",
    "preferred_label": "Prospective Registration",
    "normalized_label": "prospective_registration",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100016",
    "category_label": "Research Transparency and Reporting Completeness",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100016",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of prospective registration.",
    "what_it_measures": "Assesses prospective registration using evidence appropriate to research transparency and reporting completeness, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in prospective registration can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Study report / dataset / evidence package",
    "applicable_study_types_source": "All biomedical study reports and data releases",
    "related_frameworks_source": "EQUATOR; PRISMA; CONSORT; STROBE; STARD; TRIPOD; CARE; CHEERS",
    "closely_related_metrics_source": "Protocol Availability; Prespecified Analysis Adherence; Outcome Definition Completeness",
    "common_misinterpretations": "Treating prospective registration as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Study report / dataset / evidence package",
    "study_type_applicability": "All biomedical study reports and data releases",
    "domain_applicability": "Research Transparency and Reporting Completeness",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000425",
    "api_endpoint_template": "/v1/metrics/BEMO:2000425/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000425_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 432,
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    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 432; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
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    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000426",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000426",
    "preferred_label": "Protocol Availability",
    "normalized_label": "protocol_availability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100016",
    "category_label": "Research Transparency and Reporting Completeness",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100016",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of protocol availability.",
    "what_it_measures": "Assesses protocol availability using evidence appropriate to research transparency and reporting completeness, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in protocol availability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Study report / dataset / evidence package",
    "applicable_study_types_source": "All biomedical study reports and data releases",
    "related_frameworks_source": "EQUATOR; PRISMA; CONSORT; STROBE; STARD; TRIPOD; CARE; CHEERS",
    "closely_related_metrics_source": "Prospective Registration; Prespecified Analysis Adherence",
    "common_misinterpretations": "Treating protocol availability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Study report / dataset / evidence package",
    "study_type_applicability": "All biomedical study reports and data releases",
    "domain_applicability": "Research Transparency and Reporting Completeness",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000426",
    "api_endpoint_template": "/v1/metrics/BEMO:2000426/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000426_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
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    "source_references": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 433; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000427",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000427",
    "preferred_label": "Quality-Control Reporting Completeness",
    "normalized_label": "quality_control_reporting_completeness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100016",
    "category_label": "Research Transparency and Reporting Completeness",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100016",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which all scientifically necessary components of quality-control reporting are present, documented, and evaluable.",
    "what_it_measures": "Assesses quality-control reporting completeness using evidence appropriate to research transparency and reporting completeness, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in quality-control reporting completeness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Study report / dataset / evidence package",
    "applicable_study_types_source": "All biomedical study reports and data releases",
    "related_frameworks_source": "EQUATOR; PRISMA; CONSORT; STROBE; STARD; TRIPOD; CARE; CHEERS",
    "closely_related_metrics_source": "Processed-Data Availability; Negative-Result Reporting; Null-Result Interpretability",
    "common_misinterpretations": "Treating quality-control reporting completeness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Study report / dataset / evidence package",
    "study_type_applicability": "All biomedical study reports and data releases",
    "domain_applicability": "Research Transparency and Reporting Completeness",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000427",
    "api_endpoint_template": "/v1/metrics/BEMO:2000427/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000427_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
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    "source_references": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 434; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000428",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000428",
    "preferred_label": "Raw-Data Availability",
    "normalized_label": "raw_data_availability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100016",
    "category_label": "Research Transparency and Reporting Completeness",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100016",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of raw-data availability.",
    "what_it_measures": "Assesses raw-data availability using evidence appropriate to research transparency and reporting completeness, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in raw-data availability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Study report / dataset / evidence package",
    "applicable_study_types_source": "All biomedical study reports and data releases",
    "related_frameworks_source": "EQUATOR; PRISMA; CONSORT; STROBE; STARD; TRIPOD; CARE; CHEERS",
    "closely_related_metrics_source": "Metadata Completeness; Processed-Data Availability; Quality-Control Reporting Completeness",
    "common_misinterpretations": "Treating raw-data availability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Study report / dataset / evidence package",
    "study_type_applicability": "All biomedical study reports and data releases",
    "domain_applicability": "Research Transparency and Reporting Completeness",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000428",
    "api_endpoint_template": "/v1/metrics/BEMO:2000428/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000428_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 435,
    "source_record_hash": "2fcf4f96e7ca202f61d3de161ead38ea506d30ac8f05b66ac8a84b27f3da645e",
    "source_references": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 435; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "obo_subset": "bemo_reproducibility_replication_and_research_transparency",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000429",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000429",
    "preferred_label": "Recruitment Reporting Completeness",
    "normalized_label": "recruitment_reporting_completeness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100016",
    "category_label": "Research Transparency and Reporting Completeness",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100016",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which all scientifically necessary components of recruitment reporting are present, documented, and evaluable.",
    "what_it_measures": "Assesses recruitment reporting completeness using evidence appropriate to research transparency and reporting completeness, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in recruitment reporting completeness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Study report / dataset / evidence package",
    "applicable_study_types_source": "All biomedical study reports and data releases",
    "related_frameworks_source": "EQUATOR; PRISMA; CONSORT; STROBE; STARD; TRIPOD; CARE; CHEERS",
    "closely_related_metrics_source": "Eligibility Criteria Completeness; Participant Flow Completeness; Harms Reporting Completeness",
    "common_misinterpretations": "Treating recruitment reporting completeness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Study report / dataset / evidence package",
    "study_type_applicability": "All biomedical study reports and data releases",
    "domain_applicability": "Research Transparency and Reporting Completeness",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000429",
    "api_endpoint_template": "/v1/metrics/BEMO:2000429/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000429_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
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    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
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    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
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    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
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    "metric_id": "BEMO:2000430",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000430",
    "preferred_label": "Reproducibility Information Completeness",
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    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
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    "category_label": "Research Transparency and Reporting Completeness",
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    "modified_date": "2026-08-02",
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    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
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    "why_it_matters": "Material weakness in reproducibility information completeness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Study report / dataset / evidence package",
    "applicable_study_types_source": "All biomedical study reports and data releases",
    "related_frameworks_source": "EQUATOR; PRISMA; CONSORT; STROBE; STARD; TRIPOD; CARE; CHEERS",
    "closely_related_metrics_source": "Deviations-from-Protocol Transparency",
    "common_misinterpretations": "Treating reproducibility information completeness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Established within specialty",
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    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
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    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
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    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
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    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Study report / dataset / evidence package",
    "study_type_applicability": "All biomedical study reports and data releases",
    "domain_applicability": "Research Transparency and Reporting Completeness",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
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    "provenance_model": "W3C PROV-O",
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    "curator": "Unassigned",
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    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 437; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
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    "xrefs": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
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    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
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  {
    "metric_id": "BEMO:2000431",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000431",
    "preferred_label": "Statistical Methods Reporting Completeness",
    "normalized_label": "statistical_methods_reporting_completeness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000004",
    "pillar_label": "Reproducibility, Replication, and Research Transparency",
    "category_id": "BEMO:1100016",
    "category_label": "Research Transparency and Reporting Completeness",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100016",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
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    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which all scientifically necessary components of statistical methods reporting are present, documented, and evaluable.",
    "what_it_measures": "Assesses statistical methods reporting completeness using evidence appropriate to research transparency and reporting completeness, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in statistical methods reporting completeness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Study report / dataset / evidence package",
    "applicable_study_types_source": "All biomedical study reports and data releases",
    "related_frameworks_source": "EQUATOR; PRISMA; CONSORT; STROBE; STARD; TRIPOD; CARE; CHEERS",
    "closely_related_metrics_source": "Harms Reporting Completeness; Missing-Data Reporting Completeness; Funding-Source Transparency",
    "common_misinterpretations": "Treating statistical methods reporting completeness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Established within specialty",
    "maturity_of_metric": "Established",
    "references_source": "https://www.equator-network.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.equator-network.org/reporting-guidelines/stard/ | https://www.tripod-statement.org/ | https://www.care-statement.org/ | https://www.equator-network.org/reporting-guidelines/cheers/",
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    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
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    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
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    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
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    "notes": "No source scientific statement was silently altered or replaced."
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    "abbreviation": "",
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    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
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    "lifecycle_status": "Candidate",
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    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
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    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
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    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Fragility Index; Posterior Probability Strength; Prior Sensitivity",
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    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
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    "output_datatype": "xsd:anySimpleType",
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    "maximum_value": null,
    "null_value": null,
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    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
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    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
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    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
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    "study_type_applicability": "All quantitative biomedical studies",
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    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 439; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000433",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000433",
    "preferred_label": "Calibration of Statistical Predictions",
    "normalized_label": "calibration_of_statistical_predictions",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of calibration of statistical predictions.",
    "what_it_measures": "Assesses calibration of statistical predictions using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in calibration of statistical predictions can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Measurement Error Correction; Discrimination of Statistical Predictions; Decision-Curve Net Benefit",
    "common_misinterpretations": "Treating calibration of statistical predictions as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000433",
    "api_endpoint_template": "/v1/metrics/BEMO:2000433/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000433_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 440,
    "source_record_hash": "1d5cbda1b0dc5b30aa8339e6219d08168170bd684f74bf0679b26dd4ece9ead4",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 440; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000434",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000434",
    "preferred_label": "Clinical Relevance of Effect",
    "normalized_label": "clinical_relevance_of_effect",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of clinical relevance of effect.",
    "what_it_measures": "Assesses clinical relevance of effect using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in clinical relevance of effect can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Decision-Curve Net Benefit; Fragility Index; Bayes Factor Evidence",
    "common_misinterpretations": "Treating clinical relevance of effect as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000434",
    "api_endpoint_template": "/v1/metrics/BEMO:2000434/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000434_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 441,
    "source_record_hash": "7e04bf59de003d9389f3d5e5a39c09dbec7b25b54fdd665e24d339ccf148fb17",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 441; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000435",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000435",
    "preferred_label": "Confidence Interval Compatibility",
    "normalized_label": "confidence_interval_compatibility",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The justified degree of certainty assigned to confidence interval compatibility given the quantity, quality, consistency, and limitations of supporting evidence.",
    "what_it_measures": "Assesses confidence interval compatibility using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in confidence interval compatibility can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Estimate Precision; Statistical Power; Type I Error Control",
    "common_misinterpretations": "Treating confidence interval compatibility as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000435",
    "api_endpoint_template": "/v1/metrics/BEMO:2000435/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000435_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 442,
    "source_record_hash": "4b44e65362db0ef8f1ef0ae6eb87b631fd22642d5790f792ab6c3d6a9a693508",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 442; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000436",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000436",
    "preferred_label": "Decision-Curve Net Benefit",
    "normalized_label": "decision_curve_net_benefit",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of decision-curve net benefit.",
    "what_it_measures": "Assesses decision-curve net benefit using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in decision-curve net benefit can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Discrimination of Statistical Predictions; Clinical Relevance of Effect; Fragility Index",
    "common_misinterpretations": "Treating decision-curve net benefit as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000436",
    "api_endpoint_template": "/v1/metrics/BEMO:2000436/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000436_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 443,
    "source_record_hash": "7e96f3c494e389efab04f0ca564863ebd840cadeaf424446d3f94ddb483ed76c",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 443; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000437",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000437",
    "preferred_label": "Discrimination of Statistical Predictions",
    "normalized_label": "discrimination_of_statistical_predictions",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of discrimination of statistical predictions.",
    "what_it_measures": "Assesses discrimination of statistical predictions using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in discrimination of statistical predictions can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Calibration of Statistical Predictions; Decision-Curve Net Benefit; Clinical Relevance of Effect",
    "common_misinterpretations": "Treating discrimination of statistical predictions as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000437",
    "api_endpoint_template": "/v1/metrics/BEMO:2000437/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000437_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 444,
    "source_record_hash": "cf100cd63561a5d7a167b9d561a196b9309ca048456a8705766e76a54a524fce",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 444; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000438",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000438",
    "preferred_label": "Distributional Assumption Adequacy",
    "normalized_label": "distributional_assumption_adequacy",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which distributional assumption is sufficient and fit for the stated biomedical inference.",
    "what_it_measures": "Assesses distributional assumption adequacy using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in distributional assumption adequacy can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Residual Diagnostics Adequacy; Variance Estimation Validity; Missing-Data Mechanism Plausibility",
    "common_misinterpretations": "Treating distributional assumption adequacy as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000438",
    "api_endpoint_template": "/v1/metrics/BEMO:2000438/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000438_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 445,
    "source_record_hash": "79608c041c0babc1613cca804b9e22a2fcbadbeabfda7d7b0bf2336528db7db1",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 445; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000439",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000439",
    "preferred_label": "Effect Magnitude",
    "normalized_label": "effect_magnitude",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of effect magnitude.",
    "what_it_measures": "Assesses effect magnitude using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in effect magnitude can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Estimate Precision; Confidence Interval Compatibility",
    "common_misinterpretations": "Treating effect magnitude as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000439",
    "api_endpoint_template": "/v1/metrics/BEMO:2000439/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000439_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 446,
    "source_record_hash": "e21896fd55cc8da1ecb273cc15de195832d87a4d4554d2b68b3a9ce060442d84",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 446; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000440",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000440",
    "preferred_label": "Equivalence Margin Validity",
    "normalized_label": "equivalence_margin_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which equivalence margin supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses equivalence margin validity using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in equivalence margin validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Prior Sensitivity; Noninferiority Margin Validity",
    "common_misinterpretations": "Treating equivalence margin validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000440",
    "api_endpoint_template": "/v1/metrics/BEMO:2000440/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000440_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 447,
    "source_record_hash": "226b21fe561d36c12bfde0bcc47bb1ad6cb02760533a4b768747d6a0ab92184b",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 447; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000441",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000441",
    "preferred_label": "Estimate Precision",
    "normalized_label": "estimate_precision",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The closeness of repeated estimates or measurements and the narrowness of uncertainty around estimate.",
    "what_it_measures": "Assesses estimate precision using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in estimate precision can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Effect Magnitude; Confidence Interval Compatibility; Statistical Power",
    "common_misinterpretations": "Treating estimate precision as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000441",
    "api_endpoint_template": "/v1/metrics/BEMO:2000441/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000441_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 448,
    "source_record_hash": "9458d6e4371d11a80963339d3a9a6c5dcc187a36080cf18d964ecb5827c41820",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 448; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000442",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000442",
    "preferred_label": "Fragility Index",
    "normalized_label": "fragility_index",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of fragility index.",
    "what_it_measures": "Assesses fragility index using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in fragility index can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Clinical Relevance of Effect; Bayes Factor Evidence; Posterior Probability Strength",
    "common_misinterpretations": "Treating fragility index as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000442",
    "api_endpoint_template": "/v1/metrics/BEMO:2000442/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000442_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 449,
    "source_record_hash": "045c39ed086cc31d598f1fe91547a90170ea8cc0b684f22d5338144e750a0843",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 449; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000443",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000443",
    "preferred_label": "Imputation Validity",
    "normalized_label": "imputation_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which imputation supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses imputation validity using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in imputation validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Missing-Data Sensitivity; Outlier Influence Robustness; Influential Observation Sensitivity",
    "common_misinterpretations": "Treating imputation validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000443",
    "api_endpoint_template": "/v1/metrics/BEMO:2000443/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000443_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 450,
    "source_record_hash": "451bb1f13aa8cd7feb728a231f72c948355ace1a73de7f1903381352517ceaf5",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 450; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000444",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000444",
    "preferred_label": "Influential Observation Sensitivity",
    "normalized_label": "influential_observation_sensitivity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of influential observation sensitivity.",
    "what_it_measures": "Assesses influential observation sensitivity using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in influential observation sensitivity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified threshold; valid reference standard; complete 2×2 classification; confidence intervals; spectrum and prevalence assessment.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Outlier Influence Robustness; Nonlinearity Assessment; Interaction Assessment Adequacy",
    "common_misinterpretations": "Treating influential observation sensitivity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000444",
    "api_endpoint_template": "/v1/metrics/BEMO:2000444/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000444_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 451,
    "source_record_hash": "0202d30b443e9ba2dd8ad4597c8e7b9fcc240af0f60b19db4a115b1d2866e858",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 451; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000445",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000445",
    "preferred_label": "Interaction Assessment Adequacy",
    "normalized_label": "interaction_assessment_adequacy",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which interaction assessment is sufficient and fit for the stated biomedical inference.",
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    "why_it_matters": "Material weakness in interaction assessment adequacy can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Nonlinearity Assessment; Overadjustment Bias Risk; Measurement Error Correction",
    "common_misinterpretations": "Treating interaction assessment adequacy as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000445",
    "api_endpoint_template": "/v1/metrics/BEMO:2000445/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000445_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
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    "source_record_hash": "7942499ba472159741e9410722d92887d17131b3d661f12b98b8ec8f2d490791",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 452; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000446",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000446",
    "preferred_label": "Measurement Error Correction",
    "normalized_label": "measurement_error_correction",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of measurement error correction.",
    "what_it_measures": "Assesses measurement error correction using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in measurement error correction can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Overadjustment Bias Risk; Calibration of Statistical Predictions; Discrimination of Statistical Predictions",
    "common_misinterpretations": "Treating measurement error correction as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000446",
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    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000446_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
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    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 453; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000447",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000447",
    "preferred_label": "Missing-Data Mechanism Plausibility",
    "normalized_label": "missing_data_mechanism_plausibility",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of missing-data mechanism plausibility.",
    "what_it_measures": "Assesses missing-data mechanism plausibility using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in missing-data mechanism plausibility can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Variance Estimation Validity; Missing-Data Sensitivity; Imputation Validity",
    "common_misinterpretations": "Treating missing-data mechanism plausibility as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000447",
    "api_endpoint_template": "/v1/metrics/BEMO:2000447/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000447_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 454,
    "source_record_hash": "399e0c1d410c7ca1c5cc767b5afb9291915d1ee3db3b4d7314b2092c6d4765e1",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 454; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
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    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000448",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000448",
    "preferred_label": "Missing-Data Sensitivity",
    "normalized_label": "missing_data_sensitivity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of missing-data sensitivity.",
    "what_it_measures": "Assesses missing-data sensitivity using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in missing-data sensitivity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified threshold; valid reference standard; complete 2×2 classification; confidence intervals; spectrum and prevalence assessment.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Missing-Data Mechanism Plausibility; Imputation Validity; Outlier Influence Robustness",
    "common_misinterpretations": "Treating missing-data sensitivity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000448",
    "api_endpoint_template": "/v1/metrics/BEMO:2000448/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000448_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 455,
    "source_record_hash": "6708217d617153345c000ff0b34cc96bd34facf9514e5d1a84b3e56623ffb545",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 455; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000449",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000449",
    "preferred_label": "Model Fit",
    "normalized_label": "model_fit",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of model fit.",
    "what_it_measures": "Assesses model fit using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in model fit can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Model Specification Adequacy; Residual Diagnostics Adequacy; Distributional Assumption Adequacy",
    "common_misinterpretations": "Treating model fit as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000449",
    "api_endpoint_template": "/v1/metrics/BEMO:2000449/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000449_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
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    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 456; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000450",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000450",
    "preferred_label": "Model Specification Adequacy",
    "normalized_label": "model_specification_adequacy",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which model specification is sufficient and fit for the stated biomedical inference.",
    "what_it_measures": "Assesses model specification adequacy using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in model specification adequacy can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Multiplicity Control; Model Fit; Residual Diagnostics Adequacy",
    "common_misinterpretations": "Treating model specification adequacy as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000450",
    "api_endpoint_template": "/v1/metrics/BEMO:2000450/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000450_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 457,
    "source_record_hash": "c5d48404d8de034fc4aa45bb9f64638b1d861e61321423aa5f11d4f63cc6783b",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 457; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000451",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000451",
    "preferred_label": "Multiplicity Control",
    "normalized_label": "multiplicity_control",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of multiplicity control.",
    "what_it_measures": "Assesses multiplicity control using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in multiplicity control can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Type II Error Risk; Model Specification Adequacy; Model Fit",
    "common_misinterpretations": "Treating multiplicity control as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000451",
    "api_endpoint_template": "/v1/metrics/BEMO:2000451/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000451_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 458,
    "source_record_hash": "282fd29ea793d9f6346d4b34598e7ca30406dad2a72b3f3167d354ca92803ec0",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 458; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000452",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000452",
    "preferred_label": "Noninferiority Margin Validity",
    "normalized_label": "noninferiority_margin_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which noninferiority margin supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses noninferiority margin validity using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in noninferiority margin validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Equivalence Margin Validity",
    "common_misinterpretations": "Treating noninferiority margin validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000452",
    "api_endpoint_template": "/v1/metrics/BEMO:2000452/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000452_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 459,
    "source_record_hash": "5c494db875d0f3ad6860a3bba83e6ac01d9f571b40aa89617a37a42c1c489cab",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 459; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000453",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000453",
    "preferred_label": "Nonlinearity Assessment",
    "normalized_label": "nonlinearity_assessment",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of nonlinearity assessment.",
    "what_it_measures": "Assesses nonlinearity assessment using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in nonlinearity assessment can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Replicate dilution series; blank and spiked samples; reference materials; method-comparison studies; predefined CLSI/ISO acceptance criteria.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Influential Observation Sensitivity; Interaction Assessment Adequacy; Overadjustment Bias Risk",
    "common_misinterpretations": "Treating nonlinearity assessment as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000453",
    "api_endpoint_template": "/v1/metrics/BEMO:2000453/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000453_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 460,
    "source_record_hash": "aec401720de6539460ff9d49f62284a772b28790802eda1b3dc7c5fc2d67af3f",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 460; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000454",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000454",
    "preferred_label": "Outlier Influence Robustness",
    "normalized_label": "outlier_influence_robustness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of outlier influence robustness.",
    "what_it_measures": "Assesses outlier influence robustness using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in outlier influence robustness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Imputation Validity; Influential Observation Sensitivity; Nonlinearity Assessment",
    "common_misinterpretations": "Treating outlier influence robustness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000454",
    "api_endpoint_template": "/v1/metrics/BEMO:2000454/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000454_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 461,
    "source_record_hash": "3a52b33f3faa79b95100ff084b9c7ca54158523c656fcaf5c298f073960428c9",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 461; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000455",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000455",
    "preferred_label": "Overadjustment Bias Risk",
    "normalized_label": "overadjustment_bias_risk",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that overadjustment bias introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses overadjustment bias risk using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in overadjustment bias risk can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Interaction Assessment Adequacy; Measurement Error Correction; Calibration of Statistical Predictions",
    "common_misinterpretations": "Treating overadjustment bias risk as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000455",
    "api_endpoint_template": "/v1/metrics/BEMO:2000455/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000455_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 462,
    "source_record_hash": "20f394b3ef37b7c0b5d8426ebcce5fe9f9ef841bbb2622101174fbb411ab7957",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 462; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000456",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000456",
    "preferred_label": "Posterior Probability Strength",
    "normalized_label": "posterior_probability_strength",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The magnitude and credibility of independent evidence supporting posterior probability.",
    "what_it_measures": "Assesses posterior probability strength using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in posterior probability strength can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Bayes Factor Evidence; Prior Sensitivity; Equivalence Margin Validity",
    "common_misinterpretations": "Treating posterior probability strength as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000456",
    "api_endpoint_template": "/v1/metrics/BEMO:2000456/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000456_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 463,
    "source_record_hash": "8a96194c8b8e65d04df266b282704e480656791b819df12c8c4924c984b02272",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 463; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000457",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000457",
    "preferred_label": "Prior Sensitivity",
    "normalized_label": "prior_sensitivity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of prior sensitivity.",
    "what_it_measures": "Assesses prior sensitivity using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in prior sensitivity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified threshold; valid reference standard; complete 2×2 classification; confidence intervals; spectrum and prevalence assessment.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Posterior Probability Strength; Equivalence Margin Validity; Noninferiority Margin Validity",
    "common_misinterpretations": "Treating prior sensitivity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000457",
    "api_endpoint_template": "/v1/metrics/BEMO:2000457/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000457_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 464,
    "source_record_hash": "ced026349740f092de03ee4146894b4367dab3b43793f3aa048eac1fd782cbda",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 464; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000458",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000458",
    "preferred_label": "Residual Diagnostics Adequacy",
    "normalized_label": "residual_diagnostics_adequacy",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which residual diagnostics is sufficient and fit for the stated biomedical inference.",
    "what_it_measures": "Assesses residual diagnostics adequacy using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in residual diagnostics adequacy can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Model Fit; Distributional Assumption Adequacy; Variance Estimation Validity",
    "common_misinterpretations": "Treating residual diagnostics adequacy as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000458",
    "api_endpoint_template": "/v1/metrics/BEMO:2000458/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000458_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 465,
    "source_record_hash": "1193234e513641f836d7ad506af2e69fb2fcba17a604fff5710f7b53f487ad89",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 465; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000459",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000459",
    "preferred_label": "Statistical Power",
    "normalized_label": "statistical_power",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of statistical power.",
    "what_it_measures": "Assesses statistical power using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in statistical power can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Confidence Interval Compatibility; Type I Error Control; Type II Error Risk",
    "common_misinterpretations": "Treating statistical power as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000459",
    "api_endpoint_template": "/v1/metrics/BEMO:2000459/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000459_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 466,
    "source_record_hash": "b5866270dc0b1ae7d14dc9e42f0ff6a1d28896f404d73ddeb44c5f7fdaf6b51a",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 466; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000460",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000460",
    "preferred_label": "Type I Error Control",
    "normalized_label": "type_i_error_control",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of type i error control.",
    "what_it_measures": "Assesses type i error control using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in type i error control can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Statistical Power; Type II Error Risk; Multiplicity Control",
    "common_misinterpretations": "Treating type i error control as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000460",
    "api_endpoint_template": "/v1/metrics/BEMO:2000460/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000460_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 467,
    "source_record_hash": "a3eba05a4613d95dc796e3df689756346c4f78ac2fda1dcb4e8cf4b813a22638",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 467; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000461",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000461",
    "preferred_label": "Type II Error Risk",
    "normalized_label": "type_ii_error_risk",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that type ii error introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses type ii error risk using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in type ii error risk can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Type I Error Control; Multiplicity Control; Model Specification Adequacy",
    "common_misinterpretations": "Treating type ii error risk as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000461",
    "api_endpoint_template": "/v1/metrics/BEMO:2000461/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000461_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 468,
    "source_record_hash": "de4287424d92a6f5a119531d8abefacf3d79beff40059540425ff1afc5f1021d",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 468; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000462",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000462",
    "preferred_label": "Variance Estimation Validity",
    "normalized_label": "variance_estimation_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100017",
    "category_label": "Statistical Validity and Inference",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100017",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which variance estimation supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses variance estimation validity using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in variance estimation validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "All quantitative biomedical studies",
    "related_frameworks_source": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9",
    "closely_related_metrics_source": "Distributional Assumption Adequacy; Missing-Data Mechanism Plausibility; Missing-Data Sensitivity",
    "common_misinterpretations": "Treating variance estimation validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "All quantitative biomedical studies",
    "domain_applicability": "Statistical Validity and Inference",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000462",
    "api_endpoint_template": "/v1/metrics/BEMO:2000462/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000462_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 469,
    "source_record_hash": "43a84aea1ea6cc79814a3121476a165954a222aece0c751b1ff5414b40efbe28",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 469; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.tripod-statement.org/ | https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/ | https://database.ich.org/sites/default/files/E9_Guideline.pdf",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000463",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000463",
    "preferred_label": "Adherence Integrity",
    "normalized_label": "adherence_integrity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100018",
    "category_label": "Study Design and Internal Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100018",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of adherence integrity.",
    "what_it_measures": "Assesses adherence integrity using evidence appropriate to study design and internal validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in adherence integrity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "related_frameworks_source": "CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI",
    "closely_related_metrics_source": "Early Stopping Bias Risk; Exposure Classification Validity; Intervention Classification Validity",
    "common_misinterpretations": "Treating adherence integrity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "domain_applicability": "Study Design and Internal Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000463",
    "api_endpoint_template": "/v1/metrics/BEMO:2000463/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000463_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 470,
    "source_record_hash": "9a20a1494ccbc46d7bc0acd4d260241ebc29edd15b77d8ccc525c9f0dba8e8de",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 470; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000464",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000464",
    "preferred_label": "Allocation Concealment",
    "normalized_label": "allocation_concealment",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100018",
    "category_label": "Study Design and Internal Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100018",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of allocation concealment.",
    "what_it_measures": "Assesses allocation concealment using evidence appropriate to study design and internal validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in allocation concealment can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "related_frameworks_source": "CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI",
    "closely_related_metrics_source": "Randomization Integrity; Baseline Comparability; Blinding Integrity",
    "common_misinterpretations": "Treating allocation concealment as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "domain_applicability": "Study Design and Internal Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000464",
    "api_endpoint_template": "/v1/metrics/BEMO:2000464/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000464_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 471,
    "source_record_hash": "3367e7e58461dcb460260b263a504d906f8c26af8608d0cf2767790d3843a2e7",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 471; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000465",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000465",
    "preferred_label": "Attrition Bias Risk",
    "normalized_label": "attrition_bias_risk",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100018",
    "category_label": "Study Design and Internal Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100018",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that attrition bias introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses attrition bias risk using evidence appropriate to study design and internal validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in attrition bias risk can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "related_frameworks_source": "CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI",
    "closely_related_metrics_source": "Detection Bias Risk; Selective Outcome Reporting Risk; Protocol Deviation Risk",
    "common_misinterpretations": "Treating attrition bias risk as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "domain_applicability": "Study Design and Internal Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000465",
    "api_endpoint_template": "/v1/metrics/BEMO:2000465/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000465_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 472,
    "source_record_hash": "0783cbbb1a7caf7ef448d6830ae564e73010beb87e2e08710ddb494b6b76ccb3",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 472; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000466",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000466",
    "preferred_label": "Baseline Comparability",
    "normalized_label": "baseline_comparability",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100018",
    "category_label": "Study Design and Internal Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100018",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of baseline comparability.",
    "what_it_measures": "Assesses baseline comparability using evidence appropriate to study design and internal validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in baseline comparability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "related_frameworks_source": "CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI",
    "closely_related_metrics_source": "Allocation Concealment; Blinding Integrity; Performance Bias Risk",
    "common_misinterpretations": "Treating baseline comparability as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "domain_applicability": "Study Design and Internal Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000466",
    "api_endpoint_template": "/v1/metrics/BEMO:2000466/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000466_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 473,
    "source_record_hash": "93fad13257c869638e96dc16ab4687d4b955a0d40d8d10736f49f12cebec65eb",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 473; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000467",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000467",
    "preferred_label": "Blinding Integrity",
    "normalized_label": "blinding_integrity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100018",
    "category_label": "Study Design and Internal Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100018",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of blinding integrity.",
    "what_it_measures": "Assesses blinding integrity using evidence appropriate to study design and internal validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in blinding integrity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "related_frameworks_source": "CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI",
    "closely_related_metrics_source": "Baseline Comparability; Performance Bias Risk; Detection Bias Risk",
    "common_misinterpretations": "Treating blinding integrity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "domain_applicability": "Study Design and Internal Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000467",
    "api_endpoint_template": "/v1/metrics/BEMO:2000467/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000467_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 474,
    "source_record_hash": "4e84b980ded4e833e93013ba317d5857e2211ad9b612e4b77eb9308cf8244573",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 474; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000468",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000468",
    "preferred_label": "Carryover Effect Risk",
    "normalized_label": "carryover_effect_risk",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100018",
    "category_label": "Study Design and Internal Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100018",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that carryover effect introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses carryover effect risk using evidence appropriate to study design and internal validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in carryover effect risk can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Replicate dilution series; blank and spiked samples; reference materials; method-comparison studies; predefined CLSI/ISO acceptance criteria.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "related_frameworks_source": "CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI",
    "closely_related_metrics_source": "Co-intervention Bias Risk; Period Effect Risk; Cluster Recruitment Bias Risk",
    "common_misinterpretations": "Treating carryover effect risk as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "domain_applicability": "Study Design and Internal Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000468",
    "api_endpoint_template": "/v1/metrics/BEMO:2000468/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000468_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 475,
    "source_record_hash": "6dbe1d75153c55efcce7da9af8dda3fe869c2f426eaaad651ee6f91b1670d205",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 475; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000469",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000469",
    "preferred_label": "Cluster Recruitment Bias Risk",
    "normalized_label": "cluster_recruitment_bias_risk",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100018",
    "category_label": "Study Design and Internal Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100018",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that cluster recruitment bias introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses cluster recruitment bias risk using evidence appropriate to study design and internal validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in cluster recruitment bias risk can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "related_frameworks_source": "CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI",
    "closely_related_metrics_source": "Period Effect Risk; Early Stopping Bias Risk; Adherence Integrity",
    "common_misinterpretations": "Treating cluster recruitment bias risk as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "domain_applicability": "Study Design and Internal Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000469",
    "api_endpoint_template": "/v1/metrics/BEMO:2000469/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000469_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 476,
    "source_record_hash": "a9882065e899d9f8a8f701c6291666b702a9ad5b769971c1d3cb596c9e39b960",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 476; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000470",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000470",
    "preferred_label": "Co-intervention Bias Risk",
    "normalized_label": "co_intervention_bias_risk",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100018",
    "category_label": "Study Design and Internal Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100018",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that co-intervention bias introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses co-intervention bias risk using evidence appropriate to study design and internal validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in co-intervention bias risk can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "related_frameworks_source": "CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI",
    "closely_related_metrics_source": "Contamination Risk; Carryover Effect Risk; Period Effect Risk",
    "common_misinterpretations": "Treating co-intervention bias risk as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "domain_applicability": "Study Design and Internal Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000470",
    "api_endpoint_template": "/v1/metrics/BEMO:2000470/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000470_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 477,
    "source_record_hash": "de36d6b209ddc70bf44fd968006b0ba61482bcc4bbe42db3c2a605301631de5e",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 477; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000471",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000471",
    "preferred_label": "Comparator Validity",
    "normalized_label": "comparator_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100018",
    "category_label": "Study Design and Internal Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100018",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which comparator supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses comparator validity using evidence appropriate to study design and internal validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in comparator validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "related_frameworks_source": "CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI",
    "closely_related_metrics_source": "Intervention Classification Validity; Control Group Appropriateness; Temporal Precedence",
    "common_misinterpretations": "Treating comparator validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "domain_applicability": "Study Design and Internal Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000471",
    "api_endpoint_template": "/v1/metrics/BEMO:2000471/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000471_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 478,
    "source_record_hash": "de06a641ed9f64a7c11259e9a1d1346140c2469d57bbd106c6257d947909a5a3",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 478; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000472",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000472",
    "preferred_label": "Contamination Risk",
    "normalized_label": "contamination_risk",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100018",
    "category_label": "Study Design and Internal Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100018",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that contamination introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses contamination risk using evidence appropriate to study design and internal validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in contamination risk can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "related_frameworks_source": "CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI",
    "closely_related_metrics_source": "Protocol Deviation Risk; Co-intervention Bias Risk; Carryover Effect Risk",
    "common_misinterpretations": "Treating contamination risk as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "domain_applicability": "Study Design and Internal Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000472",
    "api_endpoint_template": "/v1/metrics/BEMO:2000472/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000472_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 479,
    "source_record_hash": "eed78db6e72161c41f0a51c8bc55e5d20b0d6675373ef1a7bf65b4c5b0dc75c0",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 479; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000473",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000473",
    "preferred_label": "Control Group Appropriateness",
    "normalized_label": "control_group_appropriateness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100018",
    "category_label": "Study Design and Internal Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100018",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which control group is sufficient and fit for the stated biomedical inference.",
    "what_it_measures": "Assesses control group appropriateness using evidence appropriate to study design and internal validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in control group appropriateness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "related_frameworks_source": "CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI",
    "closely_related_metrics_source": "Comparator Validity; Temporal Precedence; Study Design Appropriateness",
    "common_misinterpretations": "Treating control group appropriateness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "domain_applicability": "Study Design and Internal Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000473",
    "api_endpoint_template": "/v1/metrics/BEMO:2000473/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000473_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 480,
    "source_record_hash": "47dcb7d2162b3c8496d326c0cd9b9dfbef0e0b4032c2c7d93f31f67139c5990f",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 480; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000474",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000474",
    "preferred_label": "Detection Bias Risk",
    "normalized_label": "detection_bias_risk",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100018",
    "category_label": "Study Design and Internal Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100018",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that detection bias introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses detection bias risk using evidence appropriate to study design and internal validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in detection bias risk can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "related_frameworks_source": "CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI",
    "closely_related_metrics_source": "Performance Bias Risk; Attrition Bias Risk; Selective Outcome Reporting Risk",
    "common_misinterpretations": "Treating detection bias risk as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "domain_applicability": "Study Design and Internal Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000474",
    "api_endpoint_template": "/v1/metrics/BEMO:2000474/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000474_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 481,
    "source_record_hash": "98c36b49fe475eec66359fae3b2440fc1429c378e2bbe5896e082ec203855535",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 481; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000475",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000475",
    "preferred_label": "Differential Follow-up Risk",
    "normalized_label": "differential_follow_up_risk",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100018",
    "category_label": "Study Design and Internal Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100018",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that differential follow-up introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses differential follow-up risk using evidence appropriate to study design and internal validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in differential follow-up risk can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "related_frameworks_source": "CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI",
    "closely_related_metrics_source": "Follow-up Completeness",
    "common_misinterpretations": "Treating differential follow-up risk as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "domain_applicability": "Study Design and Internal Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000475",
    "api_endpoint_template": "/v1/metrics/BEMO:2000475/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000475_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 482,
    "source_record_hash": "ccfe7e445aeb97f5f6fbabfec00706b7cd315705f68e05e908e47860b40d8ad4",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 482; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000476",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000476",
    "preferred_label": "Early Stopping Bias Risk",
    "normalized_label": "early_stopping_bias_risk",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100018",
    "category_label": "Study Design and Internal Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100018",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that early stopping bias introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses early stopping bias risk using evidence appropriate to study design and internal validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in early stopping bias risk can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "related_frameworks_source": "CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI",
    "closely_related_metrics_source": "Cluster Recruitment Bias Risk; Adherence Integrity; Exposure Classification Validity",
    "common_misinterpretations": "Treating early stopping bias risk as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "domain_applicability": "Study Design and Internal Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000476",
    "api_endpoint_template": "/v1/metrics/BEMO:2000476/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000476_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 483,
    "source_record_hash": "8ac86a4a6b6a886dad127939918a466b8c70bd2b6b13b03a987aab048ac4c7c3",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 483; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000477",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000477",
    "preferred_label": "Exposure Classification Validity",
    "normalized_label": "exposure_classification_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100018",
    "category_label": "Study Design and Internal Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100018",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which exposure classification supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses exposure classification validity using evidence appropriate to study design and internal validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in exposure classification validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "related_frameworks_source": "CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI",
    "closely_related_metrics_source": "Adherence Integrity; Intervention Classification Validity; Comparator Validity",
    "common_misinterpretations": "Treating exposure classification validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "domain_applicability": "Study Design and Internal Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000477",
    "api_endpoint_template": "/v1/metrics/BEMO:2000477/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000477_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 484,
    "source_record_hash": "6d08552ad6c8b3c6d5a3c8ed35293fcfc624984197116fb158f6c3a04698789f",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 484; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000478",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000478",
    "preferred_label": "Follow-up Completeness",
    "normalized_label": "follow_up_completeness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100018",
    "category_label": "Study Design and Internal Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100018",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which all scientifically necessary components of follow-up are present, documented, and evaluable.",
    "what_it_measures": "Assesses follow-up completeness using evidence appropriate to study design and internal validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in follow-up completeness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Proportion or percentage (0–1 or 0–100%)",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "related_frameworks_source": "CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI",
    "closely_related_metrics_source": "Outcome Ascertainment Validity; Differential Follow-up Risk",
    "common_misinterpretations": "Treating follow-up completeness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 9,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ProportionScale",
    "output_datatype": "xsd:decimal",
    "unit_ontology_iri": "",
    "unit_text": "Proportion or percentage (0–1 or 0–100%)",
    "minimum_value": 0.0,
    "maximum_value": 1.0,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "QuantitativeProportionComputation",
    "computation_readiness": "TemplateComputable",
    "formula_status": "GenericTemplateDefined",
    "human_readable_formula": "value = numerator / denominator, with denominator > 0",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}",
    "required_inputs": "numerator; denominator; operational_definition; assessment_context",
    "optional_inputs": "weight; stratum; confidence_level",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; required when interpreted probabilistically.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "domain_applicability": "Study Design and Internal Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "proportion estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000478",
    "api_endpoint_template": "/v1/metrics/BEMO:2000478/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000478_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 485,
    "source_record_hash": "a99fe581309ce29c4e888ffbd9a1cba6c99a6948f2a8e99e23714e0f40920b87",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 485; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000479",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000479",
    "preferred_label": "Intervention Classification Validity",
    "normalized_label": "intervention_classification_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100018",
    "category_label": "Study Design and Internal Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100018",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which intervention classification supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses intervention classification validity using evidence appropriate to study design and internal validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in intervention classification validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "related_frameworks_source": "CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI",
    "closely_related_metrics_source": "Exposure Classification Validity; Comparator Validity; Control Group Appropriateness",
    "common_misinterpretations": "Treating intervention classification validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "domain_applicability": "Study Design and Internal Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000479",
    "api_endpoint_template": "/v1/metrics/BEMO:2000479/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000479_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 486,
    "source_record_hash": "283a3544a9dd5cb1a16190c929c82c6db2608db0f4c24860780498cb89bc0ac5",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 486; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000480",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000480",
    "preferred_label": "Outcome Ascertainment Validity",
    "normalized_label": "outcome_ascertainment_validity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100018",
    "category_label": "Study Design and Internal Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100018",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The degree to which outcome ascertainment supports the intended scientific interpretation without material systematic error.",
    "what_it_measures": "Assesses outcome ascertainment validity using evidence appropriate to study design and internal validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in outcome ascertainment validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "related_frameworks_source": "CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI",
    "closely_related_metrics_source": "Protocol Fidelity; Follow-up Completeness; Differential Follow-up Risk",
    "common_misinterpretations": "Treating outcome ascertainment validity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "domain_applicability": "Study Design and Internal Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000480",
    "api_endpoint_template": "/v1/metrics/BEMO:2000480/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000480_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 487,
    "source_record_hash": "654f73aad6650cd58d63f5a49ae9e034bfcb22952cbf7a018f652c070e1ba6c1",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 487; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000481",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000481",
    "preferred_label": "Performance Bias Risk",
    "normalized_label": "performance_bias_risk",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100018",
    "category_label": "Study Design and Internal Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100018",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that performance bias introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses performance bias risk using evidence appropriate to study design and internal validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in performance bias risk can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "related_frameworks_source": "CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI",
    "closely_related_metrics_source": "Blinding Integrity; Detection Bias Risk; Attrition Bias Risk",
    "common_misinterpretations": "Treating performance bias risk as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "domain_applicability": "Study Design and Internal Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000481",
    "api_endpoint_template": "/v1/metrics/BEMO:2000481/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000481_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 488,
    "source_record_hash": "67d1ca80d7087e3cfba7c1c9f64d45d3f4094887ac27aef09ef61bfb6d49d732",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 488; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000482",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000482",
    "preferred_label": "Period Effect Risk",
    "normalized_label": "period_effect_risk",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100018",
    "category_label": "Study Design and Internal Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100018",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that period effect introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses period effect risk using evidence appropriate to study design and internal validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in period effect risk can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "related_frameworks_source": "CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI",
    "closely_related_metrics_source": "Carryover Effect Risk; Cluster Recruitment Bias Risk; Early Stopping Bias Risk",
    "common_misinterpretations": "Treating period effect risk as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "domain_applicability": "Study Design and Internal Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000482",
    "api_endpoint_template": "/v1/metrics/BEMO:2000482/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000482_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 489,
    "source_record_hash": "78e4475c3f570e4a3e966d2bc7b940517b5d7eaa514d888dc22a6ea5b68d38fb",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 489; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000483",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000483",
    "preferred_label": "Protocol Deviation Risk",
    "normalized_label": "protocol_deviation_risk",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100018",
    "category_label": "Study Design and Internal Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100018",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that protocol deviation introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses protocol deviation risk using evidence appropriate to study design and internal validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in protocol deviation risk can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "related_frameworks_source": "CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI",
    "closely_related_metrics_source": "Selective Outcome Reporting Risk; Contamination Risk; Co-intervention Bias Risk",
    "common_misinterpretations": "Treating protocol deviation risk as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "domain_applicability": "Study Design and Internal Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000483",
    "api_endpoint_template": "/v1/metrics/BEMO:2000483/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000483_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 490,
    "source_record_hash": "7632dd2b67a9f407b6c186b3a54ef8714ff7082ed9c885957d4f06c0008e5f26",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 490; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000484",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000484",
    "preferred_label": "Protocol Fidelity",
    "normalized_label": "protocol_fidelity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100018",
    "category_label": "Study Design and Internal Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100018",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of protocol fidelity.",
    "what_it_measures": "Assesses protocol fidelity using evidence appropriate to study design and internal validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in protocol fidelity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "related_frameworks_source": "CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI",
    "closely_related_metrics_source": "Study Design Appropriateness; Outcome Ascertainment Validity; Follow-up Completeness",
    "common_misinterpretations": "Treating protocol fidelity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "domain_applicability": "Study Design and Internal Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000484",
    "api_endpoint_template": "/v1/metrics/BEMO:2000484/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000484_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 491,
    "source_record_hash": "ae404e8a9df9a665347ede4db7ae7370bdc6c77c15da3474e23c516ad81dd25e",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 491; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000485",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000485",
    "preferred_label": "Randomization Integrity",
    "normalized_label": "randomization_integrity",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100018",
    "category_label": "Study Design and Internal Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100018",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of randomization integrity.",
    "what_it_measures": "Assesses randomization integrity using evidence appropriate to study design and internal validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in randomization integrity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "related_frameworks_source": "CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI",
    "closely_related_metrics_source": "Allocation Concealment; Baseline Comparability",
    "common_misinterpretations": "Treating randomization integrity as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 10,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Mature",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Mature; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "domain_applicability": "Study Design and Internal Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000485",
    "api_endpoint_template": "/v1/metrics/BEMO:2000485/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000485_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 492,
    "source_record_hash": "8438f239c984919f366a44747e2e32efd683c0e45e3f7af6c269801f1d6694c8",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 492; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000486",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000486",
    "preferred_label": "Selective Outcome Reporting Risk",
    "normalized_label": "selective_outcome_reporting_risk",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100018",
    "category_label": "Study Design and Internal Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100018",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The probability or degree that selective outcome reporting introduces systematic distortion into a biomedical estimate or conclusion.",
    "what_it_measures": "Assesses selective outcome reporting risk using evidence appropriate to study design and internal validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in selective outcome reporting risk can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "related_frameworks_source": "CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI",
    "closely_related_metrics_source": "Attrition Bias Risk; Protocol Deviation Risk; Contamination Risk",
    "common_misinterpretations": "Treating selective outcome reporting risk as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "RiskScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal risk rating or quantitative percentage/probability; lower is generally better",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "LowerIsBetter",
    "computation_mode": "RiskAssessmentComputation",
    "computation_readiness": "RubricOrModelRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}",
    "required_inputs": "risk_factors; assessment_context; rubric_or_model_version; evidence_records",
    "optional_inputs": "weights; thresholds; calibration_dataset",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for probability outputs; rubric reliability required for ordinal outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "domain_applicability": "Study Design and Internal Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "risk assessment or calibrated probability estimation",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000486",
    "api_endpoint_template": "/v1/metrics/BEMO:2000486/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000486_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 493,
    "source_record_hash": "bcdaa5f06df0a5ab7941c490a740787093ffc20f433c48125d9c2e174850f7fd",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 493; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000487",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000487",
    "preferred_label": "Study Design Appropriateness",
    "normalized_label": "study_design_appropriateness",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100018",
    "category_label": "Study Design and Internal Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100018",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "The extent to which study design is sufficient and fit for the stated biomedical inference.",
    "what_it_measures": "Assesses study design appropriateness using evidence appropriate to study design and internal validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in study design appropriateness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Ordinal rubric, domain judgment, or normalized score",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "related_frameworks_source": "CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI",
    "closely_related_metrics_source": "Temporal Precedence; Protocol Fidelity; Outcome Ascertainment Validity",
    "common_misinterpretations": "Treating study design appropriateness as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "OrdinalOrNormalizedScoreScale",
    "output_datatype": "xsd:string_or_decimal",
    "unit_ontology_iri": "",
    "unit_text": "Ordinal rubric, domain judgment, or normalized score",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "RuleBasedRubricComputation",
    "computation_readiness": "RubricRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned, prespecified domain rubric or validated normalized scoring model.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}",
    "required_inputs": "evidence_records; assessment_context; rubric_version; operational_definition",
    "optional_inputs": "weights; thresholds; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": false,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "Required for normalized scores; inter-rater reliability required for human rubrics.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "domain_applicability": "Study Design and Internal Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "structured critical appraisal or rubric scoring",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000487",
    "api_endpoint_template": "/v1/metrics/BEMO:2000487/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000487_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 494,
    "source_record_hash": "7f9fb8e0c1ccb555a18bd7b6b07b3173d661a6707fab17a21ee632e59503b393",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 494; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  },
  {
    "metric_id": "BEMO:2000488",
    "metric_iri": "https://w3id.org/bemo/BEMO_2000488",
    "preferred_label": "Temporal Precedence",
    "normalized_label": "temporal_precedence",
    "abbreviation": "",
    "pillar_id": "BEMO:1000002",
    "pillar_label": "Study Design, Statistical Validity, and Causal Inference",
    "category_id": "BEMO:1100018",
    "category_label": "Study Design and Internal Validity",
    "parent_class_iri": "https://w3id.org/bemo/BEMO_1100018",
    "ontology_namespace": "BEMO",
    "ontology_version": "0.1.0",
    "metric_version": "1.0.0",
    "lifecycle_status": "Candidate",
    "deprecated": false,
    "replacement_id": "",
    "created_date": "2026-08-02",
    "modified_date": "2026-08-02",
    "language": "en",
    "license_status": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.",
    "scientific_definition": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of temporal precedence.",
    "what_it_measures": "Assesses temporal precedence using evidence appropriate to study design and internal validity, distinguishing random uncertainty from systematic error.",
    "why_it_matters": "Material weakness in temporal precedence can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.",
    "measurement_criteria": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.",
    "methods_of_assessment": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.",
    "units_or_scale_source": "Metric-specific continuous, categorical, or ordinal scale",
    "evidence_level_source": "Result / experiment / study / body of evidence, as applicable",
    "applicable_study_types_source": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "related_frameworks_source": "CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI",
    "closely_related_metrics_source": "Control Group Appropriateness; Study Design Appropriateness; Protocol Fidelity",
    "common_misinterpretations": "Treating temporal precedence as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.",
    "limitations": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.",
    "scientific_importance": 8,
    "frequency_of_use": "Common",
    "maturity_of_metric": "Established",
    "references_source": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "metric_kind": "AtomicOrCompositeNotYetCurated",
    "output_concept": "BEMO:0000200 Metric Assessment",
    "scale_type": "ContextDependentMixedScale",
    "output_datatype": "xsd:anySimpleType",
    "unit_ontology_iri": "",
    "unit_text": "Metric-specific continuous, categorical, or ordinal scale",
    "minimum_value": null,
    "maximum_value": null,
    "null_value": null,
    "directionality": "ContextDependentDirection",
    "computation_mode": "ContextSpecificMetricComputation",
    "computation_readiness": "OperationalDefinitionRequired",
    "formula_status": "ContextSpecificProtocolRequired",
    "human_readable_formula": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods.",
    "machine_formula_language": "BEMO-Expression-JSON",
    "machine_formula_expression": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}",
    "required_inputs": "evidence_records; assessment_context; operational_definition; computation_protocol_version",
    "optional_inputs": "weights; thresholds; reference_standard; expert_adjudication",
    "aggregation_rule": "Not specified in source; must be defined and versioned before composite use.",
    "normalization_method": "None by default; any normalization must be justified, versioned, and validated.",
    "missing_data_policy": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.",
    "uncertainty_required": true,
    "uncertainty_method": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.",
    "confidence_interval_required": true,
    "threshold_policy": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.",
    "decision_thresholds": "",
    "quality_control_requirements": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.",
    "calibration_requirement": "As applicable; mandatory for probabilistic or normalized outputs.",
    "validation_status": "Source maturity: Established; BEMO computation profile requires independent validation.",
    "benchmark_requirement": "A representative, versioned benchmark set is required before production use.",
    "gold_standard_requirement": "Use an independent reference standard when one exists; document expert-adjudicated alternatives.",
    "external_validation_required": true,
    "evidence_object_scope": "Result / experiment / study / body of evidence, as applicable",
    "study_type_applicability": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies",
    "domain_applicability": "Study Design and Internal Validity",
    "required_data_sources": "Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.",
    "computational_method_family": "metric-specific quantitative or qualitative assessment",
    "software_implementation_status": "Specification generated; metric-specific reference implementation pending.",
    "reference_implementation": "scripts/compute_metric.py --metric BEMO:2000488",
    "api_endpoint_template": "/v1/metrics/BEMO:2000488/compute",
    "json_schema_ref": "schemas/bemo-assessment.schema.json",
    "shacl_shape_iri": "https://w3id.org/bemo/shapes/BEMO_2000488_AssessmentShape",
    "provenance_model": "W3C PROV-O",
    "source_workbook": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx",
    "source_sheet": "Biomedical Evidence Metrics",
    "source_row": 495,
    "source_record_hash": "ec85a4abfc9e480fea03dfff5177f17a293899d488f06a679715de258c8591b9",
    "source_references": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "curator": "Unassigned",
    "reviewer": "Unassigned",
    "owner": "BEMO Project",
    "approval_status": "Draft",
    "governance_note": "Candidate term pending scientific, ontology-engineering, and computation-method review.",
    "editor_note": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.",
    "definition_source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 495; see source_references",
    "exact_synonyms": "",
    "broad_synonyms": "",
    "narrow_synonyms": "",
    "related_synonyms": "",
    "xrefs": "https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/ | https://www.riskofbias.info/welcome/rob-2-0-tool | https://www.riskofbias.info/welcome/home/current-version-of-robins-i | https://www.riskofbias.info/welcome/robins-e-tool | https://www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools | https://jbi.global/critical-appraisal-tools",
    "obo_subset": "bemo_study_design_statistical_validity_and_causal_inference",
    "fair_findable": "Provisional: stable local ID assigned; public namespace registration pending.",
    "fair_accessible": "Provisional: package is distributable; permanent public release location pending.",
    "fair_interoperable": "Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.",
    "fair_reusable": "Provisional: rich metadata supplied; open-license owner approval pending.",
    "confidence_in_metric_definition": "Not yet formally assessed",
    "metric_dependency_status": "Not yet curated",
    "dependency_notes": "Closely related metrics are represented; causal or computational dependencies require expert curation.",
    "implementation_notes": "Exact execution requires a validated computation profile unless formula_status is GenericTemplateDefined.",
    "test_case_status": "Generic validation template provided",
    "example_input_ref": "examples/example_metric_input.json",
    "example_output_ref": "examples/example_metric_output.jsonld",
    "notes": "No source scientific statement was silently altered or replaced."
  }
]