{"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,"maximum_value":1,"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.","url_id":"BEMO-2000060","required_inputs_list":["numerator","denominator","operational_definition","assessment_context"],"optional_inputs_list":["weight","stratum","confidence_level"],"source_record":{"source_workbook":"Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx","source_sheet":"Biomedical Evidence Metrics","source_row":"67","Category":"Biospecimen and Preanalytical Quality","Metric":"Biospecimen Provenance Completeness","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.","Typical Methods of Assessment":"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.","Units or Scale (if applicable)":"Proportion or percentage (0–1 or 0–100%)","Evidence Level Where Used":"Specimen / assay / run / laboratory / study","Applicable Study Types":"All studies using human or animal biospecimens","Related Frameworks":"BRISQ; ISO 15189; REMARK","Closely Related Metrics":"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 (1–10)":"9","Frequency of Use":"Established within specialty","Maturity of Metric":"Established","References or Origin":"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/"},"computation_profile":{"metric_id":"BEMO:2000060","preferred_label":"Biospecimen Provenance Completeness","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","output_concept":"BEMO:0000200 Metric Assessment","output_datatype":"xsd:decimal","scale_type":"ProportionScale","unit_ontology_iri":"","unit_text":"Proportion or percentage (0–1 or 0–100%)","minimum_value":0,"maximum_value":1,"null_value":null,"directionality":"ContextDependentDirection","aggregation_rule":"Not specified in source; must be defined and versioned before composite use.","normalization_method":"None by default; any normalization must be justified, versioned, and validated.","missing_data_policy":"Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.","uncertainty_required":true,"uncertainty_method":"Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.","confidence_interval_required":true,"threshold_policy":"Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without 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,"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","profile_version":"0.1.0","profile_iri":"https://w3id.org/bemo/profile/BEMO_2000060"},"relationships":[{"predicate":"closely_related_metric","source":"Source workbook: Closely Related Metrics","status":"SourceDeclared","directionality":"Directed as recorded; may be symmetric in the source","version":"0.1.0","metric_id":"BEMO:2000059","preferred_label":"Biospecimen Integrity"},{"predicate":"closely_related_metric","source":"Source workbook: Closely Related Metrics","status":"SourceDeclared","directionality":"Directed as recorded; may be symmetric in the source","version":"0.1.0","metric_id":"BEMO:2000064","preferred_label":"Collection Procedure Consistency"},{"predicate":"closely_related_metric","source":"Source workbook: Closely Related Metrics","status":"SourceDeclared","directionality":"Directed as recorded; may be symmetric in the source","version":"0.1.0","metric_id":"BEMO:2000083","preferred_label":"Warm Ischemia Control"}],"incoming_relationships":[{"predicate":"closely_related_metric","source":"Source workbook: Closely Related Metrics","status":"SourceDeclared","directionality":"Directed as recorded; may be symmetric in the source","version":"0.1.0","metric_id":"BEMO:2000059","preferred_label":"Biospecimen Integrity"},{"predicate":"closely_related_metric","source":"Source workbook: Closely Related Metrics","status":"SourceDeclared","directionality":"Directed as recorded; may be symmetric in the source","version":"0.1.0","metric_id":"BEMO:2000064","preferred_label":"Collection Procedure Consistency"}],"references":[{"order":1,"url":"https://www.equator-network.org/reporting-guidelines/brisq/","type":"Source framework, standard, guideline, or origin","verification_status":"Source-preserved; URL reachability not asserted by this package"},{"order":2,"url":"https://www.iso.org/standard/76677.html","type":"Source framework, standard, guideline, or origin","verification_status":"Source-preserved; URL reachability not asserted by this package"},{"order":3,"url":"https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumor-marker-prognostic-studies-remark/","type":"Source framework, standard, guideline, or origin","verification_status":"Source-preserved; URL reachability not asserted by this package"}]}