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denominator; operational_definition; assessment_context", "bemo:BEMO_3100007": "weight; stratum; confidence_level", "bemo:BEMO_3100008": "xsd:decimal", "bemo:BEMO_3100009": "Proportion or percentage (0–1 or 0–100%)", "bemo:BEMO_3100010": { "@type": "xsd:decimal", "@value": "0.0" }, "bemo:BEMO_3100011": { "@type": "xsd:decimal", "@value": "1.0" }, "bemo:BEMO_3100013": { "@language": "en", "@value": "Not specified in source; must be defined and versioned before composite use." }, "bemo:BEMO_3100014": { "@language": "en", "@value": "None by default; any normalization must be justified, versioned, and validated." }, "bemo:BEMO_3100015": { "@language": "en", "@value": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material." }, "bemo:BEMO_3100016": true, "bemo:BEMO_3100017": { "@language": "en", "@value": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable." }, "bemo:BEMO_3100018": true, "bemo:BEMO_3100019": { "@language": "en", "@value": "Prespecify, justify, version, and sensitivity-test thresholds; 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BEST; EMA E16; REMARK\", \"Scientific Definition\": \"A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of endpoint reliability.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Metric-specific continuous, categorical, or ordinal scale\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 49" }, { "@id": "https://w3id.org/bemo/profile/BEMO_2000117", "@type": "bemo:BEMO_0000100", "bemo:BEMO_3000007": { "@id": "bemo:BEMO_4000004" }, "bemo:BEMO_3000008": { "@id": "bemo:BEMO_4000008" }, "bemo:BEMO_3000009": { "@id": "bemo:BEMO_4000017" }, "bemo:BEMO_3000010": { "@id": "bemo:BEMO_4000019" }, "bemo:BEMO_3000011": { "@id": "bemo:BEMO_4000021" }, "bemo:BEMO_3100002": "0.1.0", "bemo:BEMO_3100003": { "@language": "en", "@value": "value = numerator / denominator, with denominator > 0" }, "bemo:BEMO_3100004": "BEMO-Expression-JSON", "bemo:BEMO_3100005": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}", "bemo:BEMO_3100006": "numerator; denominator; operational_definition; assessment_context", "bemo:BEMO_3100007": "weight; stratum; confidence_level", "bemo:BEMO_3100008": "xsd:decimal", "bemo:BEMO_3100009": "Proportion or percentage (0–1 or 0–100%)", "bemo:BEMO_3100010": { "@type": "xsd:decimal", "@value": "0.0" }, "bemo:BEMO_3100011": { "@type": "xsd:decimal", "@value": "1.0" }, "bemo:BEMO_3100013": { "@language": "en", "@value": "Not specified in source; must be defined and versioned before composite use." }, "bemo:BEMO_3100014": { "@language": "en", "@value": "None by default; any normalization must be justified, versioned, and validated." }, "bemo:BEMO_3100015": { "@language": "en", "@value": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material." }, "bemo:BEMO_3100016": true, "bemo:BEMO_3100017": { "@language": "en", "@value": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable." }, "bemo:BEMO_3100018": true, "bemo:BEMO_3100019": { "@language": "en", "@value": "Prespecify, justify, version, and sensitivity-test thresholds; 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QUADAS-2; CONSORT; STROBE\", \"Scientific Definition\": \"The degree to which ecological supports the intended scientific interpretation without material systematic error.\", \"Scientific Importance (1–10)\": \"10\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Ordinal rubric, domain judgment, or normalized score\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 203" }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/441", "@type": "prov:Entity", "bemo:BEMO_3100022": 441, "bemo:BEMO_3100023": "7e04bf59de003d9389f3d5e5a39c09dbec7b25b54fdd665e24d339ccf148fb17", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"All quantitative biomedical studies\", \"Category\": \"Statistical Validity and Inference\", \"Closely Related Metrics\": \"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.\", \"Evidence Level Where Used\": \"Result / experiment / study / body of evidence, as applicable\", \"Frequency of Use\": \"Common\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.\", \"Metric\": \"Clinical Relevance of Effect\", \"References or Origin\": \"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\", \"Related Frameworks\": \"CONSORT; STROBE; TRIPOD; REMARK; ICH E9\", \"Scientific Definition\": \"A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of clinical relevance of effect.\", \"Scientific Importance (1–10)\": \"10\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Metric-specific continuous, categorical, or ordinal scale\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 441" }, { "@id": "bemo:BEMO_2000040", "@type": "owl:Class", "bemo:BEMO_3100001": "BEMO:2000040", "bemo:BEMO_3100022": 47, "bemo:BEMO_3100023": "b87f6768315d9d24a6505cd78867a8b0dc9310fbd10aa04b46856994c12562e5", "bemo:BEMO_3100024": 10, "bemo:BEMO_3200002": { "@language": "en", "@value": "Assesses diagnostic biomarker validity using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error." }, "bemo:BEMO_3200003": { "@language": "en", "@value": "Material weakness in diagnostic biomarker validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion." }, "bemo:BEMO_3200004": { "@language": "en", "@value": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Result / experiment / study / body of evidence, as applicable" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "Biomarker development, qualification, endpoint and surrogate validation studies" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "FDA Biomarker; BEST; EMA E16; REMARK" }, "bemo:BEMO_3200011": "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/", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000040" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000048" }, { "@id": "bemo:BEMO_2000050" }, { "@id": "bemo:BEMO_2000052" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Common within specialty", "bemo:BEMO_3200020": "Mature", "obo:IAO_0000115": { "@language": "en", "@value": "The degree to which diagnostic biomarker supports the intended scientific interpretation without material systematic error." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/47" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000040", "rdfs:label": { "@language": "en", "@value": "Diagnostic Biomarker Validity" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb89" }, { "@id": "bemo:BEMO_1100002" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb89", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000040" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "bemo:BEMO_2000367", "@type": "owl:Class", "bemo:BEMO_3100001": "BEMO:2000367", "bemo:BEMO_3100022": 374, "bemo:BEMO_3100023": "beec5d62727ea3baba10451d532801205b190af60b03027284c15989d51ba1e4", "bemo:BEMO_3100024": 8, "bemo:BEMO_3200002": { "@language": "en", "@value": "Assesses isotope pattern fidelity using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error." }, "bemo:BEMO_3200003": { "@language": "en", "@value": "Material weakness in isotope pattern fidelity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion." }, "bemo:BEMO_3200004": { "@language": "en", "@value": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Result / experiment / study / body of evidence, as applicable" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "MIAPE; HUPO PSI; Metabolomics Standards" }, "bemo:BEMO_3200011": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000367" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000364" }, { "@id": "bemo:BEMO_2000368" }, { "@id": "bemo:BEMO_2000376" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Established within specialty", "bemo:BEMO_3200020": "Established", "obo:IAO_0000115": { "@language": "en", "@value": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of isotope pattern fidelity." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/374" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000367", "rdfs:label": { "@language": "en", "@value": "Isotope Pattern Fidelity" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb381" }, { "@id": "bemo:BEMO_1100014" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb381", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000367" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/384", "@type": "prov:Entity", "bemo:BEMO_3100022": 384, "bemo:BEMO_3100023": "86cf8ad175ebd274f625e908935f946750c2c41a33f40e7a8dc33224d8db7d28", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies\", \"Category\": \"Proteomics and Metabolomics\", \"Closely Related Metrics\": \"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.\", \"Evidence Level Where Used\": \"Result / experiment / study / body of evidence, as applicable\", \"Frequency of Use\": \"Established within specialty\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.\", \"Metric\": \"Protein Identification Confidence\", \"References or Origin\": \"https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/\", \"Related Frameworks\": \"MIAPE; HUPO PSI; Metabolomics Standards\", \"Scientific Definition\": \"The justified degree of certainty assigned to protein identification given the quantity, quality, consistency, and limitations of supporting evidence.\", \"Scientific Importance (1–10)\": \"10\", \"Typical Methods of Assessment\": \"Target-decoy analysis; spectral scoring; reference standards; replicate injections; retention-time and mass-error monitoring; orthogonal confirmation.\", \"Units or Scale (if applicable)\": \"Ordinal rubric, domain judgment, or normalized score\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 384" }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/109", "@type": "prov:Entity", "bemo:BEMO_3100022": 109, "bemo:BEMO_3100023": "be2ac5c0345d954f0ccc1ce41f05b792425f3fb9c158083a6db1928102b69608", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Randomized and observational etiologic studies, natural experiments, target-trial emulations\", \"Category\": \"Causal Inference\", \"Closely Related Metrics\": \"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.\", \"Evidence Level Where Used\": \"Result / experiment / study / body of evidence, as applicable\", \"Frequency of Use\": \"Established within specialty\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.\", \"Metric\": \"Positivity Adequacy\", \"References or Origin\": \"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\", \"Related Frameworks\": \"ROBINS-I; ROBINS-E; GRADE; STROBE; ICH E9\", \"Scientific Definition\": \"The extent to which positivity is sufficient and fit for the stated biomedical inference.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"Directed acyclic graphs; design emulation; balance diagnostics; negative controls; quantitative bias analysis; sensitivity and falsification analyses.\", \"Units or Scale (if applicable)\": \"Ordinal rubric, domain judgment, or normalized score\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 109" }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/274", "@type": "prov:Entity", "bemo:BEMO_3100022": 274, "bemo:BEMO_3100023": "35d988975cf78a06cb70788f89a4196551552de36a3cf47e57d2d96fc8cf41fd", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies\", \"Category\": \"Measurement and Assay Analytical Validity\", \"Closely Related Metrics\": \"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.\", \"Evidence Level Where Used\": \"Specimen / assay / run / laboratory / study\", \"Frequency of Use\": \"Common within specialty\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.\", \"Metric\": \"Accuracy\", \"References or Origin\": \"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/\", \"Related Frameworks\": \"FDA Biomarker; CLSI; ISO 15189; MIQE\", \"Scientific Definition\": \"The closeness of accuracy to the accepted reference or true value.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Metric-specific continuous, categorical, or ordinal scale\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 274" }, { "@id": "https://w3id.org/bemo/profile/BEMO_2000411", "@type": "bemo:BEMO_0000100", "bemo:BEMO_3000007": { "@id": "bemo:BEMO_4000001" }, "bemo:BEMO_3000008": { "@id": "bemo:BEMO_4000007" }, "bemo:BEMO_3000009": { "@id": "bemo:BEMO_4000014" }, "bemo:BEMO_3000010": { "@id": "bemo:BEMO_4000018" }, "bemo:BEMO_3000011": { "@id": "bemo:BEMO_4000021" }, "bemo:BEMO_3100002": "0.1.0", "bemo:BEMO_3100003": { "@language": "en", "@value": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods." }, "bemo:BEMO_3100004": "BEMO-Expression-JSON", "bemo:BEMO_3100005": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}", "bemo:BEMO_3100006": "evidence_records; assessment_context; operational_definition; computation_protocol_version", "bemo:BEMO_3100007": "weights; thresholds; reference_standard; expert_adjudication", "bemo:BEMO_3100008": "xsd:anySimpleType", "bemo:BEMO_3100009": "Metric-specific continuous, categorical, or ordinal scale", "bemo:BEMO_3100013": { "@language": "en", "@value": "Not specified in source; must be defined and versioned before composite use." }, "bemo:BEMO_3100014": { "@language": "en", "@value": "None by default; any normalization must be justified, versioned, and validated." }, "bemo:BEMO_3100015": { "@language": "en", "@value": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material." }, "bemo:BEMO_3100016": true, "bemo:BEMO_3100017": { "@language": "en", "@value": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable." }, "bemo:BEMO_3100018": true, "bemo:BEMO_3100019": { "@language": "en", "@value": "Prespecify, justify, version, and sensitivity-test thresholds; 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do not derive and evaluate on the same data without correction." }, "bemo:BEMO_3100020": { "@language": "en", "@value": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable." }, "bemo:BEMO_3100021": { "@language": "en", "@value": "As applicable; mandatory for probabilistic or normalized outputs." }, "bemo:BEMO_3100030": { "@language": "en", "@value": "Source maturity: Mature; BEMO computation profile requires independent validation." }, "dcterms:subject": { "@id": "bemo:BEMO_2000175" }, "prov:wasDerivedFrom": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/182" }, "rdfs:label": { "@language": "en", "@value": "Computation profile for Experimental Batch Randomization" } }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/377", "@type": "prov:Entity", "bemo:BEMO_3100022": 377, "bemo:BEMO_3100023": "883e5fdd2ff9e198b3ddcbafc3e6478eed144bbcc7f46c67f19ec93850e8ec4c", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies\", \"Category\": \"Proteomics and Metabolomics\", \"Closely Related Metrics\": \"Metabolite Identification Confidence; 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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.\", \"Evidence Level Where Used\": \"Result / experiment / study / body of evidence, as applicable\", \"Frequency of Use\": \"Established within specialty\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.\", \"Metric\": \"Network Context Support\", \"References or Origin\": \"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\", \"Related Frameworks\": \"GRADE; FDA Biomarker; ClinGen; OHAT; OECD\", \"Scientific Definition\": \"The magnitude and credibility of independent evidence supporting network context.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Ordinal rubric, domain judgment, or normalized score\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 23" }, { "@id": "https://w3id.org/bemo/profile/BEMO_2000465", "@type": "bemo:BEMO_0000100", "bemo:BEMO_3000007": { "@id": "bemo:BEMO_4000006" }, "bemo:BEMO_3000008": { "@id": "bemo:BEMO_4000010" }, "bemo:BEMO_3000009": { "@id": "bemo:BEMO_4000015" }, "bemo:BEMO_3000010": { "@id": "bemo:BEMO_4000018" }, "bemo:BEMO_3000011": { "@id": "bemo:BEMO_4000022" }, "bemo:BEMO_3100002": "0.1.0", "bemo:BEMO_3100003": { "@language": "en", "@value": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context." }, "bemo:BEMO_3100004": "BEMO-Expression-JSON", "bemo:BEMO_3100005": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}", "bemo:BEMO_3100006": "risk_factors; assessment_context; rubric_or_model_version; evidence_records", "bemo:BEMO_3100007": "weights; thresholds; calibration_dataset", "bemo:BEMO_3100008": "xsd:string_or_decimal", "bemo:BEMO_3100009": "Ordinal risk rating or quantitative percentage/probability; lower is generally better", "bemo:BEMO_3100013": { "@language": "en", "@value": "Not specified in source; must be defined and versioned before composite use." }, "bemo:BEMO_3100014": { "@language": "en", "@value": "None by default; any normalization must be justified, versioned, and validated." }, "bemo:BEMO_3100015": { "@language": "en", "@value": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material." }, "bemo:BEMO_3100016": true, "bemo:BEMO_3100017": { "@language": "en", "@value": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable." }, "bemo:BEMO_3100018": true, "bemo:BEMO_3100019": { "@language": "en", "@value": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction." }, "bemo:BEMO_3100020": { "@language": "en", "@value": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable." }, "bemo:BEMO_3100021": { "@language": "en", "@value": "Required for probability outputs; rubric reliability required for ordinal outputs." }, "bemo:BEMO_3100030": { "@language": "en", "@value": "Source maturity: Mature; BEMO computation profile requires independent validation." }, "dcterms:subject": { "@id": "bemo:BEMO_2000465" }, "prov:wasDerivedFrom": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/472" }, "rdfs:label": { "@language": "en", "@value": "Computation profile for Attrition Bias Risk" } }, { "@id": "https://w3id.org/bemo/profile/BEMO_2000069", "@type": "bemo:BEMO_0000100", "bemo:BEMO_3000007": { "@id": "bemo:BEMO_4000001" }, "bemo:BEMO_3000008": { "@id": "bemo:BEMO_4000007" }, "bemo:BEMO_3000009": { "@id": "bemo:BEMO_4000014" }, "bemo:BEMO_3000010": { "@id": "bemo:BEMO_4000018" }, "bemo:BEMO_3000011": { "@id": "bemo:BEMO_4000021" }, "bemo:BEMO_3100002": "0.1.0", "bemo:BEMO_3100003": { "@language": "en", "@value": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods." }, "bemo:BEMO_3100004": "BEMO-Expression-JSON", "bemo:BEMO_3100005": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}", "bemo:BEMO_3100006": "evidence_records; assessment_context; operational_definition; computation_protocol_version", "bemo:BEMO_3100007": "weights; thresholds; reference_standard; expert_adjudication", "bemo:BEMO_3100008": "xsd:anySimpleType", "bemo:BEMO_3100009": "Metric-specific continuous, categorical, or ordinal scale", "bemo:BEMO_3100013": { "@language": "en", "@value": "Not specified in source; must be defined and versioned before composite use." }, "bemo:BEMO_3100014": { "@language": "en", "@value": "None by default; any normalization must be justified, versioned, and validated." }, "bemo:BEMO_3100015": { "@language": "en", "@value": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material." }, "bemo:BEMO_3100016": true, "bemo:BEMO_3100017": { "@language": "en", "@value": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable." }, "bemo:BEMO_3100018": true, "bemo:BEMO_3100019": { "@language": "en", "@value": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction." }, "bemo:BEMO_3100020": { "@language": "en", "@value": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable." }, "bemo:BEMO_3100021": { "@language": "en", "@value": "As applicable; mandatory for probabilistic or normalized outputs." }, "bemo:BEMO_3100030": { "@language": "en", "@value": "Source maturity: Established; BEMO computation profile requires independent validation." }, "dcterms:subject": { "@id": "bemo:BEMO_2000069" }, "prov:wasDerivedFrom": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/76" }, "rdfs:label": { "@language": "en", "@value": "Computation profile for Icterus Interference" } }, { "@id": "bemo:BEMO_2000451", "@type": "owl:Class", "bemo:BEMO_3100001": "BEMO:2000451", "bemo:BEMO_3100022": 458, "bemo:BEMO_3100023": "282fd29ea793d9f6346d4b34598e7ca30406dad2a72b3f3167d354ca92803ec0", "bemo:BEMO_3100024": 8, "bemo:BEMO_3200002": { "@language": "en", "@value": "Assesses multiplicity control using evidence appropriate to statistical validity and inference, distinguishing random uncertainty from systematic error." }, "bemo:BEMO_3200003": { "@language": "en", "@value": "Material weakness in multiplicity control can change the direction, magnitude, certainty, or biological interpretation of the research conclusion." }, "bemo:BEMO_3200004": { "@language": "en", "@value": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Result / experiment / study / body of evidence, as applicable" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "All quantitative biomedical studies" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "CONSORT; STROBE; TRIPOD; REMARK; ICH E9" }, "bemo:BEMO_3200011": "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", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000451" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000449" }, { "@id": "bemo:BEMO_2000450" }, { "@id": "bemo:BEMO_2000461" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Common", "bemo:BEMO_3200020": "Established", "obo:IAO_0000115": { "@language": "en", "@value": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of multiplicity control." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/458" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000451", "rdfs:label": { "@language": "en", "@value": "Multiplicity Control" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb455" }, { "@id": "bemo:BEMO_1100017" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb455", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000451" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/228", "@type": "prov:Entity", "bemo:BEMO_3100022": 228, "bemo:BEMO_3100023": "4501a0d637c0d3d7b3852d3be8f61115b2b1ac442582dd9a3ec88bd21dad9f7c", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Mendelian disease, cancer genetics, association, segregation, and functional studies\", \"Category\": \"Genetics and Variant Evidence\", \"Closely Related Metrics\": \"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.\", \"Evidence Level Where Used\": \"Result / experiment / study / body of evidence, as applicable\", \"Frequency of Use\": \"Established within specialty\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Mature\", \"Measurement Criteria\": \"Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.\", \"Metric\": \"Gene–Disease Validity\", \"References or Origin\": \"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/\", \"Related Frameworks\": \"ClinGen; ACMG AMP; STREGA; Gene Ontology\", \"Scientific Definition\": \"The degree to which gene–disease supports the intended scientific interpretation without material systematic error.\", \"Scientific Importance (1–10)\": \"10\", \"Typical Methods of Assessment\": \"ClinGen/ACMG evidence scoring; pedigree analysis; population databases; case-control data; functional assays; expert-panel review.\", \"Units or Scale (if applicable)\": \"Ordinal rubric, domain judgment, or normalized score\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 228" }, { "@id": "bemo:BEMO_2000231", "@type": "owl:Class", "bemo:BEMO_3100001": "BEMO:2000231", "bemo:BEMO_3100022": 238, "bemo:BEMO_3100023": "8e776a34bb92ed3d093c7eb03481f1c61ce724a0995235355586c28e53418e35", "bemo:BEMO_3100024": 8, "bemo:BEMO_3200002": { "@language": "en", "@value": "Assesses rna evidence strength using evidence appropriate to genetics and variant evidence, distinguishing random uncertainty from systematic error." }, "bemo:BEMO_3200003": { "@language": "en", "@value": "Material weakness in rna evidence strength can change the direction, magnitude, certainty, or biological interpretation of the research conclusion." }, "bemo:BEMO_3200004": { "@language": "en", "@value": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Result / experiment / study / body of evidence, as applicable" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "Mendelian disease, cancer genetics, association, segregation, and functional studies" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "ClinGen; ACMG AMP; STREGA; Gene Ontology" }, "bemo:BEMO_3200011": "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/", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000231" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000214" }, { "@id": "bemo:BEMO_2000227" }, { "@id": "bemo:BEMO_2000233" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Established within specialty", "bemo:BEMO_3200020": "Established", "obo:IAO_0000115": { "@language": "en", "@value": "The magnitude and credibility of independent evidence supporting rna evidence." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/238" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000231", "rdfs:label": { "@language": "en", "@value": "RNA Evidence Strength" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb259" }, { "@id": "bemo:BEMO_1100009" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb259", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000231" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/490", "@type": "prov:Entity", "bemo:BEMO_3100022": 490, "bemo:BEMO_3100023": "7632dd2b67a9f407b6c186b3a54ef8714ff7082ed9c885957d4f06c0008e5f26", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies\", \"Category\": \"Study Design and Internal Validity\", \"Closely Related Metrics\": \"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.\", \"Evidence Level Where Used\": \"Result / experiment / study / body of evidence, as applicable\", \"Frequency of Use\": \"Common\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.\", \"Metric\": \"Protocol Deviation Risk\", \"References or Origin\": \"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\", \"Related Frameworks\": \"CONSORT; 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appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Target-decoy analysis; spectral scoring; reference standards; replicate injections; retention-time and mass-error monitoring; orthogonal confirmation." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Result / experiment / study / body of evidence, as applicable" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "MIAPE; 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appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Result / experiment / study / body of evidence, as applicable" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "All quantitative biomedical studies" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "CONSORT; 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OHAT; FDA Biomarker; EMA E16\", \"Scientific Definition\": \"A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of lowest-observed-adverse-effect level robustness.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Ordinal rubric, domain judgment, or normalized score\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 348" }, { "@id": "https://w3id.org/bemo/profile/BEMO_2000088", "@type": "bemo:BEMO_0000100", "bemo:BEMO_3000007": { "@id": "bemo:BEMO_4000006" }, "bemo:BEMO_3000008": { "@id": "bemo:BEMO_4000010" }, "bemo:BEMO_3000009": { "@id": "bemo:BEMO_4000015" }, "bemo:BEMO_3000010": { "@id": "bemo:BEMO_4000018" }, "bemo:BEMO_3000011": { "@id": "bemo:BEMO_4000022" }, "bemo:BEMO_3100002": "0.1.0", "bemo:BEMO_3100003": { "@language": "en", "@value": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context." }, "bemo:BEMO_3100004": "BEMO-Expression-JSON", "bemo:BEMO_3100005": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}", "bemo:BEMO_3100006": "risk_factors; assessment_context; rubric_or_model_version; evidence_records", "bemo:BEMO_3100007": "weights; thresholds; calibration_dataset", "bemo:BEMO_3100008": "xsd:string_or_decimal", "bemo:BEMO_3100009": "Ordinal risk rating or quantitative percentage/probability; lower is generally better", "bemo:BEMO_3100013": { "@language": "en", "@value": "Not specified in source; must be defined and versioned before composite use." }, "bemo:BEMO_3100014": { "@language": "en", "@value": "None by default; any normalization must be justified, versioned, and validated." }, "bemo:BEMO_3100015": { "@language": "en", "@value": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material." }, "bemo:BEMO_3100016": true, "bemo:BEMO_3100017": { "@language": "en", "@value": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable." }, "bemo:BEMO_3100018": true, "bemo:BEMO_3100019": { "@language": "en", "@value": "Prespecify, justify, version, and sensitivity-test thresholds; 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appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Dataset / model / pathway / network / evidence body" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "Integrated omics, networks, pathways, mechanistic and dynamic systems models" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "Gene Ontology; 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independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Ordinal rubric, domain judgment, or normalized score\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 299" }, { "@id": "https://w3id.org/bemo/profile/BEMO_2000289", "@type": "bemo:BEMO_0000100", "bemo:BEMO_3000007": { "@id": "bemo:BEMO_4000001" }, "bemo:BEMO_3000008": { "@id": "bemo:BEMO_4000007" }, "bemo:BEMO_3000009": { "@id": "bemo:BEMO_4000014" }, "bemo:BEMO_3000010": { "@id": "bemo:BEMO_4000018" }, "bemo:BEMO_3000011": { "@id": "bemo:BEMO_4000021" }, "bemo:BEMO_3100002": "0.1.0", "bemo:BEMO_3100003": { "@language": "en", "@value": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods." }, "bemo:BEMO_3100004": "BEMO-Expression-JSON", "bemo:BEMO_3100005": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}", "bemo:BEMO_3100006": "evidence_records; assessment_context; operational_definition; computation_protocol_version", "bemo:BEMO_3100007": "weights; thresholds; reference_standard; expert_adjudication", "bemo:BEMO_3100008": "xsd:anySimpleType", "bemo:BEMO_3100009": "Metric-specific continuous, categorical, or ordinal scale", "bemo:BEMO_3100013": { "@language": "en", "@value": "Not specified in source; must be defined and versioned before composite use." }, "bemo:BEMO_3100014": { "@language": "en", "@value": "None by default; any normalization must be justified, versioned, and validated." }, "bemo:BEMO_3100015": { "@language": "en", "@value": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material." }, "bemo:BEMO_3100016": true, "bemo:BEMO_3100017": { "@language": "en", "@value": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable." }, "bemo:BEMO_3100018": true, "bemo:BEMO_3100019": { "@language": "en", "@value": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction." }, "bemo:BEMO_3100020": { "@language": "en", "@value": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable." }, "bemo:BEMO_3100021": { "@language": "en", "@value": "As applicable; mandatory for probabilistic or normalized outputs." }, "bemo:BEMO_3100030": { "@language": "en", "@value": "Source maturity: Established; BEMO computation profile requires independent validation." }, "dcterms:subject": { "@id": "bemo:BEMO_2000289" }, "prov:wasDerivedFrom": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/296" }, "rdfs:label": { "@language": "en", "@value": "Computation profile for Measurement Uncertainty" } }, { "@id": "bemo:BEMO_2000369", "@type": "owl:Class", "bemo:BEMO_3100001": "BEMO:2000369", "bemo:BEMO_3100022": 376, "bemo:BEMO_3100023": "521bf8b7c1bbe892685e95c05cc7d63a05c4e26119e9951d705ff460b3bb99d1", "bemo:BEMO_3100024": 10, "bemo:BEMO_3200002": { "@language": "en", "@value": "Assesses metabolic feature reproducibility using evidence appropriate to proteomics and metabolomics, distinguishing random uncertainty from systematic error." }, "bemo:BEMO_3200003": { "@language": "en", "@value": "Material weakness in metabolic feature reproducibility can change the direction, magnitude, certainty, or biological interpretation of the research conclusion." }, "bemo:BEMO_3200004": { "@language": "en", "@value": "Independent repeats; 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HUPO PSI; Metabolomics Standards" }, "bemo:BEMO_3200011": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000369" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000359" }, { "@id": "bemo:BEMO_2000360" }, { "@id": "bemo:BEMO_2000373" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Established within specialty", "bemo:BEMO_3200020": "Established", "obo:IAO_0000115": { "@language": "en", "@value": "The degree to which metabolic feature reproducibility yields concordant results under the specified repeated-analysis or repeated-measurement conditions." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/376" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000369", "rdfs:label": { "@language": "en", "@value": "Metabolic Feature Reproducibility" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb383" }, { "@id": "bemo:BEMO_1100014" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb383", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000369" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/337", "@type": "prov:Entity", "bemo:BEMO_3100022": 337, "bemo:BEMO_3100023": "43d4a4ce7127bc52167a879f611c41413072f25e775dbe7c9446cf4028783b10", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies\", \"Category\": \"Pharmacology and Toxicology\", \"Closely Related Metrics\": \"Lowest-Observed-Adverse-Effect Level Robustness; 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direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Body of evidence / synthesis / outcome" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "Systematic reviews, meta-analyses, evidence profiles, guidelines" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "GRADE; 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HUPO PSI; Metabolomics Standards\", \"Scientific Definition\": \"A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of pathway enrichment robustness.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Ordinal rubric, domain judgment, or normalized score\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 380" }, { "@id": "bemo:BEMO_2000418", "@type": "owl:Class", "bemo:BEMO_3100001": "BEMO:2000418", "bemo:BEMO_3100022": 425, "bemo:BEMO_3100023": "810e02862dfc4630d6f7a0d7bd830ccd305d847e2d0153cfdb863b68f1c2ece8", "bemo:BEMO_3100024": 9, "bemo:BEMO_3200002": { "@language": "en", "@value": "Assesses missing-data reporting completeness using evidence appropriate to research transparency and reporting completeness, distinguishing random uncertainty from systematic error." }, "bemo:BEMO_3200003": { "@language": "en", "@value": "Material weakness in missing-data reporting completeness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion." }, "bemo:BEMO_3200004": { "@language": "en", "@value": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Study report / dataset / evidence package" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "All biomedical study reports and data releases" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "EQUATOR; PRISMA; CONSORT; STROBE; STARD; TRIPOD; CARE; CHEERS" }, "bemo:BEMO_3200011": "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/", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000418" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000409" }, { "@id": "bemo:BEMO_2000413" }, { "@id": "bemo:BEMO_2000431" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Established within specialty", "bemo:BEMO_3200020": "Established", "obo:IAO_0000115": { "@language": "en", "@value": "The extent to which all scientifically necessary components of missing-data reporting are present, documented, and evaluable." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/425" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000418", "rdfs:label": { "@language": "en", "@value": "Missing-Data Reporting Completeness" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb427" }, { "@id": "bemo:BEMO_1100016" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb427", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000418" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "bemo:BEMO_2000264", "@type": "owl:Class", "bemo:BEMO_3100001": "BEMO:2000264", "bemo:BEMO_3100022": 271, "bemo:BEMO_3100023": "6ac08afc8cf99d9cd5ee94bc247ff32edf260fc542fd5e27409d9c3b702afd66", "bemo:BEMO_3100024": 10, "bemo:BEMO_3200002": { "@language": "en", "@value": "Assesses strand bias using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error." }, "bemo:BEMO_3200003": { "@language": "en", "@value": "Material weakness in strand bias can change the direction, magnitude, certainty, or biological interpretation of the research conclusion." }, "bemo:BEMO_3200004": { "@language": "en", "@value": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Read- and variant-level quality-control summaries; replicate concordance; orthogonal confirmation; benchmarking against reference materials." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Result / experiment / study / body of evidence, as applicable" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA" }, "bemo:BEMO_3200011": "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/", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000264" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000237" }, { "@id": "bemo:BEMO_2000240" }, { "@id": "bemo:BEMO_2000254" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Established within specialty", "bemo:BEMO_3200020": "Mature", "obo:IAO_0000115": { "@language": "en", "@value": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of strand bias." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/271" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000264", "rdfs:label": { "@language": "en", "@value": "Strand Bias" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb288" }, { "@id": "bemo:BEMO_1100010" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb288", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000264" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "bemo:BEMO_2000129", "@type": "owl:Class", "bemo:BEMO_3100001": "BEMO:2000129", "bemo:BEMO_3100022": 136, "bemo:BEMO_3100023": "6a8e54c8d71bbaa2bc8361d6fc19eb1f50b8f4acd2b6d09e2b648f2337fa9298", "bemo:BEMO_3100024": 8, "bemo:BEMO_3200002": { "@language": "en", "@value": "Assesses prognostic added value using evidence appropriate to diagnostic and prognostic evidence, distinguishing random uncertainty from systematic error." }, "bemo:BEMO_3200003": { "@language": "en", "@value": "Material weakness in prognostic added value can change the direction, magnitude, certainty, or biological interpretation of the research conclusion." }, "bemo:BEMO_3200004": { "@language": "en", "@value": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Result / experiment / study / body of evidence, as applicable" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "QUADAS-2; STARD; TRIPOD; REMARK" }, "bemo:BEMO_3200011": "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/", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000129" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000124" }, { "@id": "bemo:BEMO_2000132" }, { "@id": "bemo:BEMO_2000137" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Common within specialty", "bemo:BEMO_3200020": "Established", "obo:IAO_0000115": { "@language": "en", "@value": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of prognostic added value." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/136" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000129", "rdfs:label": { "@language": "en", "@value": "Prognostic Added Value" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb168" }, { "@id": "bemo:BEMO_1100005" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb168", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000129" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "https://w3id.org/bemo/profile/BEMO_2000361", "@type": "bemo:BEMO_0000100", "bemo:BEMO_3000007": { "@id": "bemo:BEMO_4000004" }, "bemo:BEMO_3000008": { "@id": "bemo:BEMO_4000008" }, "bemo:BEMO_3000009": { "@id": "bemo:BEMO_4000017" }, "bemo:BEMO_3000010": { "@id": "bemo:BEMO_4000019" }, "bemo:BEMO_3000011": { "@id": "bemo:BEMO_4000021" }, "bemo:BEMO_3100002": "0.1.0", "bemo:BEMO_3100003": { "@language": "en", "@value": "value = numerator / denominator, with denominator > 0" }, "bemo:BEMO_3100004": "BEMO-Expression-JSON", "bemo:BEMO_3100005": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}", "bemo:BEMO_3100006": "numerator; denominator; operational_definition; assessment_context", "bemo:BEMO_3100007": "weight; stratum; confidence_level", "bemo:BEMO_3100008": "xsd:decimal", "bemo:BEMO_3100009": "Proportion or percentage (0–1 or 0–100%)", "bemo:BEMO_3100010": { "@type": "xsd:decimal", "@value": "0.0" }, "bemo:BEMO_3100011": { "@type": "xsd:decimal", "@value": "1.0" }, "bemo:BEMO_3100013": { "@language": "en", "@value": "Not specified in source; must be defined and versioned before composite use." }, "bemo:BEMO_3100014": { "@language": "en", "@value": "None by default; any normalization must be justified, versioned, and validated." }, "bemo:BEMO_3100015": { "@language": "en", "@value": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material." }, "bemo:BEMO_3100016": true, "bemo:BEMO_3100017": { "@language": "en", "@value": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable." }, "bemo:BEMO_3100018": true, "bemo:BEMO_3100019": { "@language": "en", "@value": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction." }, "bemo:BEMO_3100020": { "@language": "en", "@value": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable." }, "bemo:BEMO_3100021": { "@language": "en", "@value": "As applicable; required when interpreted probabilistically." }, "bemo:BEMO_3100030": { "@language": "en", "@value": "Source maturity: Established; BEMO computation profile requires independent validation." }, "dcterms:subject": { "@id": "bemo:BEMO_2000361" }, "prov:wasDerivedFrom": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/368" }, "rdfs:label": { "@language": "en", "@value": "Computation profile for Dynamic Range Coverage" } }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/212", "@type": "prov:Entity", "bemo:BEMO_3100022": 212, "bemo:BEMO_3100023": "39b818e971de479787fde11a4523a1b0d31f5dcbc88f645b968cff60fa6bf381", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Clinical, epidemiologic, diagnostic, translational, and population studies\", \"Category\": \"External Validity and Applicability\", \"Closely Related Metrics\": \"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.\", \"Evidence Level Where Used\": \"Body of evidence / synthesis / outcome\", \"Frequency of Use\": \"Established within specialty\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.\", \"Metric\": \"Sampling Frame Adequacy\", \"References or Origin\": \"https://www.gradeworkinggroup.org/ | https://pubmed.ncbi.nlm.nih.gov/22007046/ | https://www.consort-spirit.org/ | https://www.equator-network.org/reporting-guidelines/strobe/\", \"Related Frameworks\": \"GRADE; QUADAS-2; CONSORT; STROBE\", \"Scientific Definition\": \"The extent to which sampling frame is sufficient and fit for the stated biomedical inference.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Ordinal rubric, domain judgment, or normalized score\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 212" }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/381", "@type": "prov:Entity", "bemo:BEMO_3100022": 381, "bemo:BEMO_3100023": "7f78eede8aa05781dde3f12d7ea8111e1c0b552f5b722c402b0de5323e65b0ea", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies\", \"Category\": \"Proteomics and Metabolomics\", \"Closely Related Metrics\": \"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.\", \"Evidence Level Where Used\": \"Result / experiment / study / body of evidence, as applicable\", \"Frequency of Use\": \"Established within specialty\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.\", \"Metric\": \"Peptide Identification Confidence\", \"References or Origin\": \"https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/\", \"Related Frameworks\": \"MIAPE; HUPO PSI; Metabolomics Standards\", \"Scientific Definition\": \"The justified degree of certainty assigned to peptide identification given the quantity, quality, consistency, and limitations of supporting evidence.\", \"Scientific Importance (1–10)\": \"10\", \"Typical Methods of Assessment\": \"Target-decoy analysis; spectral scoring; reference standards; replicate injections; retention-time and mass-error monitoring; orthogonal confirmation.\", \"Units or Scale (if applicable)\": \"Ordinal rubric, domain judgment, or normalized score\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 381" }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/77", "@type": "prov:Entity", "bemo:BEMO_3100022": 77, "bemo:BEMO_3100023": "572ca1cf50802a5447be4c1286cdad2930a7ec08e97e7b9af663a3cb66e1d788", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"All studies using human or animal biospecimens\", \"Category\": \"Biospecimen and Preanalytical Quality\", \"Closely Related Metrics\": \"Hemolysis Burden; 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OHAT; FDA Biomarker; EMA E16" }, "bemo:BEMO_3200011": "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", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000339" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000343" }, { "@id": "bemo:BEMO_2000354" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Established within specialty", "bemo:BEMO_3200020": "Established", "obo:IAO_0000115": { "@language": "en", "@value": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of human-relevance of toxicological evidence." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/346" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000339", "rdfs:label": { "@language": "en", "@value": "Human-Relevance of Toxicological Evidence" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb356" }, { "@id": "bemo:BEMO_1100013" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb356", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000339" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/122", "@type": "prov:Entity", "bemo:BEMO_3100022": 122, "bemo:BEMO_3100023": "a903f03627bce43e756f3c1d10c27c552a53bce0346a40196ea1cd72afe63de0", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies\", \"Category\": \"Diagnostic and Prognostic Evidence\", \"Closely Related Metrics\": \"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.\", \"Evidence Level Where Used\": \"Result / experiment / study / body of evidence, as applicable\", \"Frequency of Use\": \"Common within specialty\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.\", \"Metric\": \"Diagnostic Odds Ratio\", \"References or Origin\": \"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/\", \"Related Frameworks\": \"QUADAS-2; STARD; TRIPOD; REMARK\", \"Scientific Definition\": \"A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of diagnostic odds ratio.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"Two-by-two tables; binomial confidence intervals; hierarchical diagnostic meta-analysis; threshold and prevalence analyses.\", \"Units or Scale (if applicable)\": \"Ratio scale; null typically 1\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 122" }, { "@id": "bemo:BEMO_2000163", "@type": "owl:Class", "bemo:BEMO_3100001": "BEMO:2000163", "bemo:BEMO_3100022": 170, "bemo:BEMO_3100023": "8c42609174eeba28064b2f75bd158a40f97b17f9cdaa32aed81219eddf87ef89", "bemo:BEMO_3100024": 8, "bemo:BEMO_3200002": { "@language": "en", "@value": "Assesses selective nonreporting risk using evidence appropriate to evidence certainty and synthesis, distinguishing random uncertainty from systematic error." }, "bemo:BEMO_3200003": { "@language": "en", "@value": "Material weakness in selective nonreporting risk can change the direction, magnitude, certainty, or biological interpretation of the research conclusion." }, "bemo:BEMO_3200004": { "@language": "en", "@value": "Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Body of evidence / synthesis / outcome" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "Systematic reviews, meta-analyses, evidence profiles, guidelines" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "GRADE; PRISMA; AMSTAR 2; RoB" }, "bemo:BEMO_3200011": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000163" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000162" }, { "@id": "bemo:BEMO_2000164" }, { "@id": "bemo:BEMO_2000165" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Common", "bemo:BEMO_3200020": "Established", "obo:IAO_0000115": { "@language": "en", "@value": "The probability or degree that selective nonreporting introduces systematic distortion into a biomedical estimate or conclusion." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/170" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000163", "rdfs:label": { "@language": "en", "@value": "Selective Nonreporting Risk" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb199" }, { "@id": "bemo:BEMO_1100006" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb199", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000163" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/440", "@type": "prov:Entity", "bemo:BEMO_3100022": 440, "bemo:BEMO_3100023": "1d5cbda1b0dc5b30aa8339e6219d08168170bd684f74bf0679b26dd4ece9ead4", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"All quantitative biomedical studies\", \"Category\": \"Statistical Validity and Inference\", \"Closely Related Metrics\": \"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.\", \"Evidence Level Where Used\": \"Result / experiment / study / body of evidence, as applicable\", \"Frequency of Use\": \"Common\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.\", \"Metric\": \"Calibration of Statistical Predictions\", \"References or Origin\": \"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\", \"Related Frameworks\": \"CONSORT; STROBE; TRIPOD; REMARK; ICH E9\", \"Scientific Definition\": \"A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of calibration of statistical predictions.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Metric-specific continuous, categorical, or ordinal scale\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 440" }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/194", "@type": "prov:Entity", "bemo:BEMO_3100022": 194, "bemo:BEMO_3100023": "93f7de14ca784e8a47e3c6ab351c1e75c21a4c3e26305cfe63e0d4fef2122575", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"In vitro, ex vivo, organoid, animal, and preclinical experiments\", \"Category\": \"Experimental Biology and Animal Research\", \"Closely Related Metrics\": \"Animal Model Predictive Validity; 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SYRCLE; OECD\", \"Scientific Definition\": \"The extent to which species is sufficient and fit for the stated biomedical inference.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Ordinal rubric, domain judgment, or normalized score\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 194" }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/53", "@type": "prov:Entity", "bemo:BEMO_3100022": 53, "bemo:BEMO_3100023": "8e195ef346deba393b7a3adaf4c77bfbd949dbf0f057cd9af26312568cb85421", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Biomarker development, qualification, endpoint and surrogate validation studies\", \"Category\": \"Biomarker and Endpoint Validation\", \"Closely Related Metrics\": \"Biomarker Sensitivity to Change; 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BEST; EMA E16; REMARK\", \"Scientific Definition\": \"The degree to which known-groups supports the intended scientific interpretation without material systematic error.\", \"Scientific Importance (1–10)\": \"10\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Ordinal rubric, domain judgment, or normalized score\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 53" }, { "@id": "bemo:BEMO_2000467", "@type": "owl:Class", "bemo:BEMO_3100001": "BEMO:2000467", "bemo:BEMO_3100022": 474, "bemo:BEMO_3100023": "4e84b980ded4e833e93013ba317d5857e2211ad9b612e4b77eb9308cf8244573", "bemo:BEMO_3100024": 8, "bemo:BEMO_3200002": { "@language": "en", "@value": "Assesses blinding integrity using evidence appropriate to study design and internal validity, distinguishing random uncertainty from systematic error." }, "bemo:BEMO_3200003": { "@language": "en", "@value": "Material weakness in blinding integrity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion." }, "bemo:BEMO_3200004": { "@language": "en", "@value": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Result / experiment / study / body of evidence, as applicable" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI" }, "bemo:BEMO_3200011": "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", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000467" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000466" }, { "@id": "bemo:BEMO_2000474" }, { "@id": "bemo:BEMO_2000481" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Common", "bemo:BEMO_3200020": "Established", "obo:IAO_0000115": { "@language": "en", "@value": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of blinding integrity." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/474" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000467", "rdfs:label": { "@language": "en", "@value": "Blinding Integrity" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb469" }, { "@id": "bemo:BEMO_1100018" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb469", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000467" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "https://w3id.org/bemo/profile/BEMO_2000217", "@type": "bemo:BEMO_0000100", "bemo:BEMO_3000007": { "@id": "bemo:BEMO_4000002" }, "bemo:BEMO_3000008": { "@id": "bemo:BEMO_4000011" }, "bemo:BEMO_3000009": { "@id": "bemo:BEMO_4000016" }, "bemo:BEMO_3000010": { "@id": "bemo:BEMO_4000018" }, "bemo:BEMO_3000011": { "@id": "bemo:BEMO_4000021" }, "bemo:BEMO_3100002": "0.1.0", "bemo:BEMO_3100003": { "@language": "en", "@value": "Apply a versioned, prespecified domain rubric or validated normalized scoring model." }, "bemo:BEMO_3100004": "BEMO-Expression-JSON", "bemo:BEMO_3100005": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}", "bemo:BEMO_3100006": "evidence_records; 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appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Body of evidence / synthesis / outcome" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "Clinical, epidemiologic, diagnostic, translational, and population studies" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "GRADE; 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assessment_context; rubric_version; operational_definition", "bemo:BEMO_3100007": "weights; thresholds; expert_adjudication", "bemo:BEMO_3100008": "xsd:string_or_decimal", "bemo:BEMO_3100009": "Ordinal rubric, domain judgment, or normalized score", "bemo:BEMO_3100013": { "@language": "en", "@value": "Not specified in source; must be defined and versioned before composite use." }, "bemo:BEMO_3100014": { "@language": "en", "@value": "None by default; any normalization must be justified, versioned, and validated." }, "bemo:BEMO_3100015": { "@language": "en", "@value": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material." }, "bemo:BEMO_3100016": true, "bemo:BEMO_3100017": { "@language": "en", "@value": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable." }, "bemo:BEMO_3100018": false, "bemo:BEMO_3100019": { "@language": "en", "@value": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction." }, "bemo:BEMO_3100020": { "@language": "en", "@value": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable." }, "bemo:BEMO_3100021": { "@language": "en", "@value": "Required for normalized scores; inter-rater reliability required for human rubrics." }, "bemo:BEMO_3100030": { "@language": "en", "@value": "Source maturity: Mature; BEMO computation profile requires independent validation." }, "dcterms:subject": { "@id": "bemo:BEMO_2000272" }, "prov:wasDerivedFrom": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/279" }, "rdfs:label": { "@language": "en", "@value": "Computation profile for Analytical Validity" } }, { "@id": "bemo:BEMO_4000014", "@type": [ "owl:NamedIndividual", "bemo:BEMO_0000402" ], "obo:IAO_0000115": { "@language": "en", "@value": "Controlled BEMO ComputationReadinessStatus value: OperationalDefinitionRequired." }, "oboInOwl:id": "BEMO:4000014", "rdfs:label": { "@language": "en", "@value": "Operational Definition Required" }, "skos:notation": "OperationalDefinitionRequired" }, { "@id": "bemo:BEMO_2000170", "@type": "owl:Class", "bemo:BEMO_3100001": "BEMO:2000170", "bemo:BEMO_3100022": 177, "bemo:BEMO_3100023": "bfb6735bf1e0494f94802ec087edc274ccdaea50558f3ea043f6f21ae9210505", "bemo:BEMO_3100024": 8, "bemo:BEMO_3200002": { "@language": "en", "@value": "Assesses attrition accounting in animal studies using evidence appropriate to experimental biology and animal research, distinguishing random uncertainty from systematic error." }, "bemo:BEMO_3200003": { "@language": "en", "@value": "Material weakness in attrition accounting in animal studies can change the direction, magnitude, certainty, or biological interpretation of the research conclusion." }, "bemo:BEMO_3200004": { "@language": "en", "@value": "Prespecified operational definition; 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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.\", \"Evidence Level Where Used\": \"Dataset / model / pathway / network / evidence body\", \"Frequency of Use\": \"Established within specialty\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.\", \"Metric\": \"Pathway Enrichment Consistency\", \"References or Origin\": \"https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/\", \"Related Frameworks\": \"Gene Ontology; Reactome; UniProt; GA4GH\", \"Scientific Definition\": \"The degree of agreement in pathway enrichment across measurements, studies, methods, populations, or biological levels.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Metric-specific continuous, categorical, or ordinal scale\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 329" }, { "@id": "https://w3id.org/bemo/profile/BEMO_2000071", "@type": "bemo:BEMO_0000100", "bemo:BEMO_3000007": { "@id": "bemo:BEMO_4000002" }, "bemo:BEMO_3000008": { "@id": "bemo:BEMO_4000011" }, "bemo:BEMO_3000009": { "@id": "bemo:BEMO_4000016" }, "bemo:BEMO_3000010": { "@id": "bemo:BEMO_4000018" }, "bemo:BEMO_3000011": { "@id": "bemo:BEMO_4000021" }, "bemo:BEMO_3100002": "0.1.0", "bemo:BEMO_3100003": { "@language": "en", "@value": "Apply a versioned, prespecified domain rubric or validated normalized scoring model." }, "bemo:BEMO_3100004": "BEMO-Expression-JSON", "bemo:BEMO_3100005": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}", "bemo:BEMO_3100006": "evidence_records; assessment_context; rubric_version; operational_definition", "bemo:BEMO_3100007": "weights; thresholds; expert_adjudication", "bemo:BEMO_3100008": "xsd:string_or_decimal", "bemo:BEMO_3100009": "Ordinal rubric, domain judgment, or normalized score", "bemo:BEMO_3100013": { "@language": "en", "@value": "Not specified in source; must be defined and versioned before composite use." }, "bemo:BEMO_3100014": { "@language": "en", "@value": "None by default; any normalization must be justified, versioned, and validated." }, "bemo:BEMO_3100015": { "@language": "en", "@value": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material." }, "bemo:BEMO_3100016": true, "bemo:BEMO_3100017": { "@language": "en", "@value": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable." }, "bemo:BEMO_3100018": false, "bemo:BEMO_3100019": { "@language": "en", "@value": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction." }, "bemo:BEMO_3100020": { "@language": "en", "@value": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable." }, "bemo:BEMO_3100021": { "@language": "en", "@value": "Required for normalized scores; inter-rater reliability required for human rubrics." }, "bemo:BEMO_3100030": { "@language": "en", "@value": "Source maturity: Established; BEMO computation profile requires independent validation." }, "dcterms:subject": { "@id": "bemo:BEMO_2000071" }, "prov:wasDerivedFrom": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/78" }, "rdfs:label": { "@language": "en", "@value": "Computation profile for Matched-Sample Integrity" } }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/89", "@type": "prov:Entity", "bemo:BEMO_3100022": 89, "bemo:BEMO_3100023": "e7836bb1f6728d199c8634dbdbf560dae6243a3932920cc82164935a37c9180e", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"All studies using human or animal biospecimens\", \"Category\": \"Biospecimen and Preanalytical Quality\", \"Closely Related Metrics\": \"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.\", \"Evidence Level Where Used\": \"Specimen / assay / run / laboratory / study\", \"Frequency of Use\": \"Established within specialty\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.\", \"Metric\": \"Tumor Purity\", \"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/\", \"Related Frameworks\": \"BRISQ; ISO 15189; REMARK\", \"Scientific Definition\": \"A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of tumor purity.\", \"Scientific Importance (1–10)\": \"8\", \"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%)\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 89" }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/412", "@type": "prov:Entity", "bemo:BEMO_3100022": 412, "bemo:BEMO_3100023": "60121a2998efa943018d3ff7dd4130d4332ee279da0e8111b650ea175e9dacce", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"All experimental, computational, clinical, and omics studies\", \"Category\": \"Reproducibility and Replication\", \"Closely Related Metrics\": \"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.\", \"Evidence Level Where Used\": \"Result / experiment / study / body of evidence, as applicable\", \"Frequency of Use\": \"Established within specialty\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.\", \"Metric\": \"Result Reproducibility\", \"References or Origin\": \"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\", \"Related Frameworks\": \"PRISMA; CONSORT; MIAME; MINSEQE; MIAPE; ARRIVE 2.0\", \"Scientific Definition\": \"The degree to which result reproducibility yields concordant results under the specified repeated-analysis or repeated-measurement conditions.\", \"Scientific Importance (1–10)\": \"10\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Metric-specific continuous, categorical, or ordinal scale\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 412" }, { "@id": "https://w3id.org/bemo/profile/BEMO_2000468", "@type": "bemo:BEMO_0000100", "bemo:BEMO_3000007": { "@id": "bemo:BEMO_4000006" }, "bemo:BEMO_3000008": { "@id": "bemo:BEMO_4000010" }, "bemo:BEMO_3000009": { "@id": "bemo:BEMO_4000015" }, "bemo:BEMO_3000010": { "@id": "bemo:BEMO_4000018" }, "bemo:BEMO_3000011": { "@id": "bemo:BEMO_4000022" }, "bemo:BEMO_3100002": "0.1.0", "bemo:BEMO_3100003": { "@language": "en", "@value": "Apply a versioned risk rubric or calibrated probability model defined for the metric and context." }, "bemo:BEMO_3100004": "BEMO-Expression-JSON", "bemo:BEMO_3100005": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_risk_category\",\"probability\",\"percentage\"]}", "bemo:BEMO_3100006": "risk_factors; assessment_context; rubric_or_model_version; evidence_records", "bemo:BEMO_3100007": "weights; thresholds; calibration_dataset", "bemo:BEMO_3100008": "xsd:string_or_decimal", "bemo:BEMO_3100009": "Ordinal risk rating or quantitative percentage/probability; lower is generally better", "bemo:BEMO_3100013": { "@language": "en", "@value": "Not specified in source; must be defined and versioned before composite use." }, "bemo:BEMO_3100014": { "@language": "en", "@value": "None by default; any normalization must be justified, versioned, and validated." }, "bemo:BEMO_3100015": { "@language": "en", "@value": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material." }, "bemo:BEMO_3100016": true, "bemo:BEMO_3100017": { "@language": "en", "@value": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable." }, "bemo:BEMO_3100018": true, "bemo:BEMO_3100019": { "@language": "en", "@value": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction." }, "bemo:BEMO_3100020": { "@language": "en", "@value": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable." }, "bemo:BEMO_3100021": { "@language": "en", "@value": "Required for probability outputs; rubric reliability required for ordinal outputs." }, "bemo:BEMO_3100030": { "@language": "en", "@value": "Source maturity: Established; BEMO computation profile requires independent validation." }, "dcterms:subject": { "@id": "bemo:BEMO_2000468" }, "prov:wasDerivedFrom": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/475" }, "rdfs:label": { "@language": "en", "@value": "Computation profile for Carryover Effect Risk" } }, { "@id": "bemo:BEMO_2000050", "@type": "owl:Class", "bemo:BEMO_3100001": "BEMO:2000050", "bemo:BEMO_3100022": 57, "bemo:BEMO_3100023": "4eb497c772907b7927e32ee929fba9a804b1c75888594041caa61dfab977440a", "bemo:BEMO_3100024": 10, "bemo:BEMO_3200002": { "@language": "en", "@value": "Assesses pharmacodynamic biomarker validity using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error." }, "bemo:BEMO_3200003": { "@language": "en", "@value": "Material weakness in pharmacodynamic biomarker validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion." }, "bemo:BEMO_3200004": { "@language": "en", "@value": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Result / experiment / study / body of evidence, as applicable" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "Biomarker development, qualification, endpoint and surrogate validation studies" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "FDA Biomarker; BEST; EMA E16; REMARK" }, "bemo:BEMO_3200011": "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/", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000050" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000040" }, { "@id": "bemo:BEMO_2000048" }, { "@id": "bemo:BEMO_2000054" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Common within specialty", "bemo:BEMO_3200020": "Mature", "obo:IAO_0000115": { "@language": "en", "@value": "The degree to which pharmacodynamic biomarker supports the intended scientific interpretation without material systematic error." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/57" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000050", "rdfs:label": { "@language": "en", "@value": "Pharmacodynamic Biomarker Validity" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb98" }, { "@id": "bemo:BEMO_1100002" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb98", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000050" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/375", "@type": "prov:Entity", "bemo:BEMO_3100022": 375, "bemo:BEMO_3100023": "ebb0e828e6a056d20bce6788aee10b743cfcc2fc175a82fd693585711880ff73", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies\", \"Category\": \"Proteomics and Metabolomics\", \"Closely Related Metrics\": \"Retention-Time Stability; 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HUPO PSI; Metabolomics Standards\", \"Scientific Definition\": \"The closeness of mass to the accepted reference or true value.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"Target-decoy analysis; spectral scoring; reference standards; replicate injections; retention-time and mass-error monitoring; orthogonal confirmation.\", \"Units or Scale (if applicable)\": \"Metric-specific continuous, categorical, or ordinal scale\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 375" }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/139", "@type": "prov:Entity", "bemo:BEMO_3100022": 139, "bemo:BEMO_3100023": "c2720768cdf2be8ed6a3b935c205e9cb522ea1c958d036e680eee5e7cba4038e", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies\", \"Category\": \"Diagnostic and Prognostic Evidence\", \"Closely Related Metrics\": \"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.\", \"Evidence Level Where Used\": \"Result / experiment / study / body of evidence, as applicable\", \"Frequency of Use\": \"Common within specialty\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.\", \"Metric\": \"Prognostic Transportability\", \"References or Origin\": \"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/\", \"Related Frameworks\": \"QUADAS-2; STARD; TRIPOD; REMARK\", \"Scientific Definition\": \"A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of prognostic transportability.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Metric-specific continuous, categorical, or ordinal scale\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 139" }, { "@id": "https://w3id.org/bemo/profile/BEMO_2000205", "@type": "bemo:BEMO_0000100", "bemo:BEMO_3000007": { "@id": "bemo:BEMO_4000002" }, "bemo:BEMO_3000008": { "@id": "bemo:BEMO_4000011" }, "bemo:BEMO_3000009": { "@id": "bemo:BEMO_4000016" }, "bemo:BEMO_3000010": { "@id": "bemo:BEMO_4000018" }, "bemo:BEMO_3000011": { "@id": "bemo:BEMO_4000021" }, "bemo:BEMO_3100002": "0.1.0", "bemo:BEMO_3100003": { "@language": "en", "@value": "Apply a versioned, prespecified domain rubric or validated normalized scoring model." }, "bemo:BEMO_3100004": "BEMO-Expression-JSON", "bemo:BEMO_3100005": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}", "bemo:BEMO_3100006": "evidence_records; assessment_context; rubric_version; operational_definition", "bemo:BEMO_3100007": "weights; thresholds; expert_adjudication", "bemo:BEMO_3100008": "xsd:string_or_decimal", "bemo:BEMO_3100009": "Ordinal rubric, domain judgment, or normalized score", "bemo:BEMO_3100013": { "@language": "en", "@value": "Not specified in source; must be defined and versioned before composite use." }, "bemo:BEMO_3100014": { "@language": "en", "@value": "None by default; any normalization must be justified, versioned, and validated." }, "bemo:BEMO_3100015": { "@language": "en", "@value": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material." }, "bemo:BEMO_3100016": true, "bemo:BEMO_3100017": { "@language": "en", "@value": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable." }, "bemo:BEMO_3100018": false, "bemo:BEMO_3100019": { "@language": "en", "@value": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction." }, "bemo:BEMO_3100020": { "@language": "en", "@value": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable." }, "bemo:BEMO_3100021": { "@language": "en", "@value": "Required for normalized scores; inter-rater reliability required for human rubrics." }, "bemo:BEMO_3100030": { "@language": "en", "@value": "Source maturity: Established; BEMO computation profile requires independent validation." }, "dcterms:subject": { "@id": "bemo:BEMO_2000205" }, "prov:wasDerivedFrom": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/212" }, "rdfs:label": { "@language": "en", "@value": "Computation profile for Sampling Frame Adequacy" } }, { "@id": "https://w3id.org/bemo/profile/BEMO_2000240", "@type": "bemo:BEMO_0000100", "bemo:BEMO_3000007": { "@id": "bemo:BEMO_4000004" }, "bemo:BEMO_3000008": { "@id": "bemo:BEMO_4000008" }, "bemo:BEMO_3000009": { "@id": "bemo:BEMO_4000017" }, "bemo:BEMO_3000010": { "@id": "bemo:BEMO_4000019" }, "bemo:BEMO_3000011": { "@id": "bemo:BEMO_4000021" }, "bemo:BEMO_3100002": "0.1.0", "bemo:BEMO_3100003": { "@language": "en", "@value": "value = numerator / denominator, with denominator > 0" }, "bemo:BEMO_3100004": "BEMO-Expression-JSON", "bemo:BEMO_3100005": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}", "bemo:BEMO_3100006": "numerator; denominator; operational_definition; assessment_context", "bemo:BEMO_3100007": "weight; stratum; confidence_level", "bemo:BEMO_3100008": "xsd:decimal", "bemo:BEMO_3100009": "Proportion or percentage (0–1 or 0–100%)", "bemo:BEMO_3100010": { "@type": "xsd:decimal", "@value": "0.0" }, "bemo:BEMO_3100011": { "@type": "xsd:decimal", "@value": "1.0" }, "bemo:BEMO_3100013": { "@language": "en", "@value": "Not specified in source; must be defined and versioned before composite use." }, "bemo:BEMO_3100014": { "@language": "en", "@value": "None by default; any normalization must be justified, versioned, and validated." }, "bemo:BEMO_3100015": { "@language": "en", "@value": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material." }, "bemo:BEMO_3100016": true, "bemo:BEMO_3100017": { "@language": "en", "@value": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable." }, "bemo:BEMO_3100018": true, "bemo:BEMO_3100019": { "@language": "en", "@value": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction." }, "bemo:BEMO_3100020": { "@language": "en", "@value": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable." }, "bemo:BEMO_3100021": { "@language": "en", "@value": "As applicable; required when interpreted probabilistically." }, "bemo:BEMO_3100030": { "@language": "en", "@value": "Source maturity: Established; BEMO computation profile requires independent validation." }, "dcterms:subject": { "@id": "bemo:BEMO_2000240" }, "prov:wasDerivedFrom": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/247" }, "rdfs:label": { "@language": "en", "@value": "Computation profile for Call-Rate Completeness" } }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/218", "@type": "prov:Entity", "bemo:BEMO_3100022": 218, "bemo:BEMO_3100023": "2dd4a685750034c6175101f0128d889784cf621fed0cf93a74098e6b4879332b", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Mendelian disease, cancer genetics, association, segregation, and functional studies\", \"Category\": \"Genetics and Variant Evidence\", \"Closely Related Metrics\": \"De Novo Evidence Strength; 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ACMG AMP; STREGA; Gene Ontology\", \"Scientific Definition\": \"The magnitude and credibility of independent evidence supporting allelic evidence.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"ClinGen/ACMG evidence scoring; pedigree analysis; population databases; case-control data; functional assays; expert-panel review.\", \"Units or Scale (if applicable)\": \"Ordinal rubric, domain judgment, or normalized score\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 218" }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/301", "@type": "prov:Entity", "bemo:BEMO_3100022": 301, "bemo:BEMO_3100023": "66143063e8139ffa9de4cc6fb03a0eb1778bd92be05c901387fc7af071b0e433", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies\", \"Category\": \"Measurement and Assay Analytical Validity\", \"Closely Related Metrics\": \"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.\", \"Evidence Level Where Used\": \"Specimen / assay / run / laboratory / study\", \"Frequency of Use\": \"Common within specialty\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.\", \"Metric\": \"Reagent Lot Consistency\", \"References or Origin\": \"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/\", \"Related Frameworks\": \"FDA Biomarker; CLSI; ISO 15189; MIQE\", \"Scientific Definition\": \"The degree of agreement in reagent lot across measurements, studies, methods, populations, or biological levels.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Metric-specific continuous, categorical, or ordinal scale\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 301" }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/361", "@type": "prov:Entity", "bemo:BEMO_3100022": 361, "bemo:BEMO_3100023": "f3eb077ab3d21773df18d06eb29c8a11272ed7cbfe8f22da0ffedd8a171bc393", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies\", \"Category\": \"Pharmacology and Toxicology\", \"Closely Related Metrics\": \"Toxicokinetic Concordance; 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OHAT; FDA Biomarker; EMA E16\", \"Scientific Definition\": \"The degree to which species extrapolation supports the intended scientific interpretation without material systematic error.\", \"Scientific Importance (1–10)\": \"10\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Ordinal rubric, domain judgment, or normalized score\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 361" }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/113", "@type": "prov:Entity", "bemo:BEMO_3100022": 113, "bemo:BEMO_3100023": "ba5e2bde29a386ccb9cae3afe1f1c9476a350f65371bc1aebd58a3579e6e702c", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Randomized and observational etiologic studies, natural experiments, target-trial emulations\", \"Category\": \"Causal Inference\", \"Closely Related Metrics\": \"Reverse-Causation Risk; 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do not derive and evaluate on the same data without correction." }, "bemo:BEMO_3100020": { "@language": "en", "@value": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable." }, "bemo:BEMO_3100021": { "@language": "en", "@value": "As applicable; mandatory for probabilistic or normalized outputs." }, "bemo:BEMO_3100030": { "@language": "en", "@value": "Source maturity: Established; BEMO computation profile requires independent validation." }, "dcterms:subject": { "@id": "bemo:BEMO_2000294" }, "prov:wasDerivedFrom": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/301" }, "rdfs:label": { "@language": "en", "@value": "Computation profile for Reagent Lot Consistency" } }, { "@id": "bemo:BEMO_2000081", "@type": "owl:Class", "bemo:BEMO_3100001": "BEMO:2000081", "bemo:BEMO_3100022": 88, "bemo:BEMO_3100023": "81f1c97831f3ffbcc8b4e89c16604f987d3fa2baac750496d710981c68a60598", "bemo:BEMO_3100024": 8, "bemo:BEMO_3200002": { "@language": "en", "@value": "Assesses transport condition integrity using evidence appropriate to biospecimen and preanalytical quality, distinguishing random uncertainty from systematic error." }, "bemo:BEMO_3200003": { "@language": "en", "@value": "Material weakness in transport condition integrity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion." }, "bemo:BEMO_3200004": { "@language": "en", "@value": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Specimen / assay / run / laboratory / study" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "All studies using human or animal biospecimens" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "BRISQ; ISO 15189; REMARK" }, "bemo:BEMO_3200011": "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/", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000081" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000058" }, { "@id": "bemo:BEMO_2000067" }, { "@id": "bemo:BEMO_2000076" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Established within specialty", "bemo:BEMO_3200020": "Established", "obo:IAO_0000115": { "@language": "en", "@value": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of transport condition integrity." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/88" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000081", "rdfs:label": { "@language": "en", "@value": "Transport Condition Integrity" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb126" }, { "@id": "bemo:BEMO_1100003" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb126", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000081" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "bemo:BEMO_2000487", "@type": "owl:Class", "bemo:BEMO_3100001": "BEMO:2000487", "bemo:BEMO_3100022": 494, "bemo:BEMO_3100023": "7f9fb8e0c1ccb555a18bd7b6b07b3173d661a6707fab17a21ee632e59503b393", "bemo:BEMO_3100024": 8, "bemo:BEMO_3200002": { "@language": "en", "@value": "Assesses study design appropriateness using evidence appropriate to study design and internal validity, distinguishing random uncertainty from systematic error." }, "bemo:BEMO_3200003": { "@language": "en", "@value": "Material weakness in study design appropriateness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion." }, "bemo:BEMO_3200004": { "@language": "en", "@value": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Result / experiment / study / body of evidence, as applicable" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI" }, "bemo:BEMO_3200011": "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", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000487" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000480" }, { "@id": "bemo:BEMO_2000484" }, { "@id": "bemo:BEMO_2000488" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Common", "bemo:BEMO_3200020": "Established", "obo:IAO_0000115": { "@language": "en", "@value": "The extent to which study design is sufficient and fit for the stated biomedical inference." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/494" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000487", "rdfs:label": { "@language": "en", "@value": "Study Design Appropriateness" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb487" }, { "@id": "bemo:BEMO_1100018" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb487", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000487" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/362", "@type": "prov:Entity", "bemo:BEMO_3100022": 362, "bemo:BEMO_3100023": "34f5d4730ddbb7e269fc6713d96c49c0fba2d2f738ddbfb47d339a6ed5f8cf6e", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies\", \"Category\": \"Pharmacology and Toxicology\", \"Closely Related Metrics\": \"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.\", \"Evidence Level Where Used\": \"Result / experiment / study / body of evidence, as applicable\", \"Frequency of Use\": \"Established within specialty\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.\", \"Metric\": \"Therapeutic Window Evidence\", \"References or Origin\": \"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\", \"Related Frameworks\": \"OECD; OHAT; FDA Biomarker; EMA E16\", \"Scientific Definition\": \"A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of therapeutic window evidence.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Metric-specific continuous, categorical, or ordinal scale\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 362" }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/386", "@type": "prov:Entity", "bemo:BEMO_3100022": 386, "bemo:BEMO_3100023": "8df86e86625f432ba76b927808300a9cfa4a9b6844cae40ca0c6240f4f899eda", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies\", \"Category\": \"Proteomics and Metabolomics\", \"Closely Related Metrics\": \"Post-Translational Modification Localization Confidence; 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assessment_context; rubric_version; operational_definition", "bemo:BEMO_3100007": "weights; thresholds; expert_adjudication", "bemo:BEMO_3100008": "xsd:string_or_decimal", "bemo:BEMO_3100009": "Ordinal rubric, domain judgment, or normalized score", "bemo:BEMO_3100013": { "@language": "en", "@value": "Not specified in source; must be defined and versioned before composite use." }, "bemo:BEMO_3100014": { "@language": "en", "@value": "None by default; any normalization must be justified, versioned, and validated." }, "bemo:BEMO_3100015": { "@language": "en", "@value": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material." }, "bemo:BEMO_3100016": true, "bemo:BEMO_3100017": { "@language": "en", "@value": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable." }, "bemo:BEMO_3100018": false, "bemo:BEMO_3100019": { "@language": "en", "@value": "Prespecify, justify, version, and sensitivity-test thresholds; 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do not derive and evaluate on the same data without correction." }, "bemo:BEMO_3100020": { "@language": "en", "@value": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable." }, "bemo:BEMO_3100021": { "@language": "en", "@value": "As applicable; required when interpreted probabilistically." }, "bemo:BEMO_3100030": { "@language": "en", "@value": "Source maturity: Established; BEMO computation profile requires independent validation." }, "dcterms:subject": { "@id": "bemo:BEMO_2000318" }, "prov:wasDerivedFrom": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/325" }, "rdfs:label": { "@language": "en", "@value": "Computation profile for Ontology Annotation Completeness" } }, { "@id": "bemo:BEMO_4000023", "@type": [ "owl:NamedIndividual", "bemo:BEMO_0000402" ], "obo:IAO_0000115": { "@language": "en", "@value": "Controlled BEMO LifecycleStatus value: Candidate." }, "oboInOwl:id": "BEMO:4000023", "rdfs:label": { "@language": "en", "@value": "Candidate" }, "skos:notation": "Candidate" }, { "@id": "bemo:BEMO_3000020", "@type": "owl:ObjectProperty", "obo:IAO_0000115": { "@language": "en", "@value": "Connects a metric assessment to the process that generated it." }, "oboInOwl:id": "BEMO:3000020", "owl:equivalentProperty": { "@id": "prov:wasGeneratedBy" }, "rdfs:label": { "@language": "en", "@value": "generated by computation process" }, "skos:closeMatch": { "@id": "prov:wasGeneratedBy" } }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/117", "@type": "prov:Entity", "bemo:BEMO_3100022": 117, "bemo:BEMO_3100023": "5c4feaae4c2a565042108ac4cb807678f9be09f3e84e62f596afd3338e3ceec6", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies\", \"Category\": \"Diagnostic and Prognostic Evidence\", \"Closely Related Metrics\": \"Diagnostic Odds Ratio; 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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.\", \"Evidence Level Where Used\": \"Result / experiment / study / body of evidence, as applicable\", \"Frequency of Use\": \"Established within specialty\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.\", \"Metric\": \"Metabolite Coverage\", \"References or Origin\": \"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\", \"Related Frameworks\": \"OECD; 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computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Established within specialty", "bemo:BEMO_3200020": "Established", "obo:IAO_0000115": { "@language": "en", "@value": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of data-sharing transparency." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/417" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000410", "rdfs:label": { "@language": "en", "@value": "Data-Sharing Transparency" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb419" }, { "@id": "bemo:BEMO_1100016" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb419", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000410" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "https://w3id.org/bemo/profile/BEMO_2000463", "@type": "bemo:BEMO_0000100", "bemo:BEMO_3000007": { "@id": "bemo:BEMO_4000002" }, "bemo:BEMO_3000008": { "@id": "bemo:BEMO_4000011" }, "bemo:BEMO_3000009": { "@id": "bemo:BEMO_4000016" }, "bemo:BEMO_3000010": { "@id": "bemo:BEMO_4000018" }, "bemo:BEMO_3000011": { "@id": "bemo:BEMO_4000021" }, "bemo:BEMO_3100002": "0.1.0", "bemo:BEMO_3100003": { "@language": "en", "@value": "Apply a versioned, prespecified domain rubric or validated normalized scoring model." }, "bemo:BEMO_3100004": "BEMO-Expression-JSON", "bemo:BEMO_3100005": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}", "bemo:BEMO_3100006": "evidence_records; 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do not derive and evaluate on the same data without correction." }, "bemo:BEMO_3100020": { "@language": "en", "@value": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable." }, "bemo:BEMO_3100021": { "@language": "en", "@value": "Required for normalized scores; inter-rater reliability required for human rubrics." }, "bemo:BEMO_3100030": { "@language": "en", "@value": "Source maturity: Established; BEMO computation profile requires independent validation." }, "dcterms:subject": { "@id": "bemo:BEMO_2000463" }, "prov:wasDerivedFrom": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/470" }, "rdfs:label": { "@language": "en", "@value": "Computation profile for Adherence Integrity" } }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/457", "@type": "prov:Entity", "bemo:BEMO_3100022": 457, "bemo:BEMO_3100023": "c5d48404d8de034fc4aa45bb9f64638b1d861e61321423aa5f11d4f63cc6783b", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"All quantitative biomedical studies\", \"Category\": \"Statistical Validity and Inference\", \"Closely Related Metrics\": \"Multiplicity Control; 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appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Result / experiment / study / body of evidence, as applicable" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "In vitro, ex vivo, organoid, animal, and preclinical experiments" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "ARRIVE 2.0; 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assessment_context; operational_definition; computation_protocol_version", "bemo:BEMO_3100007": "weights; thresholds; reference_standard; expert_adjudication", "bemo:BEMO_3100008": "xsd:anySimpleType", "bemo:BEMO_3100009": "Metric-specific continuous, categorical, or ordinal scale", "bemo:BEMO_3100013": { "@language": "en", "@value": "Not specified in source; must be defined and versioned before composite use." }, "bemo:BEMO_3100014": { "@language": "en", "@value": "None by default; any normalization must be justified, versioned, and validated." }, "bemo:BEMO_3100015": { "@language": "en", "@value": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material." }, "bemo:BEMO_3100016": true, "bemo:BEMO_3100017": { "@language": "en", "@value": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable." }, "bemo:BEMO_3100018": true, "bemo:BEMO_3100019": { "@language": "en", "@value": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction." }, "bemo:BEMO_3100020": { "@language": "en", "@value": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable." }, "bemo:BEMO_3100021": { "@language": "en", "@value": "As applicable; mandatory for probabilistic or normalized outputs." }, "bemo:BEMO_3100030": { "@language": "en", "@value": "Source maturity: Established; BEMO computation profile requires independent validation." }, "dcterms:subject": { "@id": "bemo:BEMO_2000432" }, "prov:wasDerivedFrom": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/439" }, "rdfs:label": { "@language": "en", "@value": "Computation profile for Bayes Factor Evidence" } }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/333", "@type": "prov:Entity", "bemo:BEMO_3100022": 333, "bemo:BEMO_3100023": "9009911ac3f6266273d49aa664b528314dd25468ab2969a5c3dfb8593502a99c", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Integrated omics, networks, pathways, mechanistic and dynamic systems models\", \"Category\": \"Multi-omics and Systems Biology\", \"Closely Related Metrics\": \"Entity Resolution Accuracy; 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direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Result / experiment / study / body of evidence, as applicable" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "CONSORT; 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traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Study report / dataset / evidence package" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "All biomedical study reports and data releases" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "EQUATOR; 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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.\", \"Evidence Level Where Used\": \"Specimen / assay / run / laboratory / study\", \"Frequency of Use\": \"Common within specialty\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.\", \"Metric\": \"Reproducibility of Measurement\", \"References or Origin\": \"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/\", \"Related Frameworks\": \"FDA Biomarker; CLSI; ISO 15189; MIQE\", \"Scientific Definition\": \"The degree to which reproducibility of measurement yields concordant results under the specified repeated-analysis or repeated-measurement conditions.\", \"Scientific Importance (1–10)\": \"10\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Metric-specific continuous, categorical, or ordinal scale\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 306" }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/340", "@type": "prov:Entity", "bemo:BEMO_3100022": 340, "bemo:BEMO_3100023": "f5636ed02b8746eb48d98671b027c695a8940399bff60ebeae8ca955d99bae6a", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies\", \"Category\": \"Pharmacology and Toxicology\", \"Closely Related Metrics\": \"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.\", \"Evidence Level Where Used\": \"Result / experiment / study / body of evidence, as applicable\", \"Frequency of Use\": \"Established within specialty\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.\", \"Metric\": \"Developmental Toxicity Evidence Strength\", \"References or Origin\": \"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\", \"Related Frameworks\": \"OECD; OHAT; FDA Biomarker; EMA E16\", \"Scientific Definition\": \"The magnitude and credibility of independent evidence supporting developmental toxicity evidence.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Ordinal rubric, domain judgment, or normalized score\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 340" }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/242", "@type": "prov:Entity", "bemo:BEMO_3100022": 242, "bemo:BEMO_3100023": "ce239eedae0622eb1018ab2bfc52cd2d32ef0a5f6a874008c2d8838deb99bd4a", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Mendelian disease, cancer genetics, association, segregation, and functional studies\", \"Category\": \"Genetics and Variant Evidence\", \"Closely Related Metrics\": \"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.\", \"Evidence Level Where Used\": \"Result / experiment / study / body of evidence, as applicable\", \"Frequency of Use\": \"Established within specialty\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.\", \"Metric\": \"Variant Pathogenicity Evidence Strength\", \"References or Origin\": \"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/\", \"Related Frameworks\": \"ClinGen; 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HUPO PSI; Metabolomics Standards" }, "bemo:BEMO_3200011": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000368" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000364" }, { "@id": "bemo:BEMO_2000367" }, { "@id": "bemo:BEMO_2000383" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Established within specialty", "bemo:BEMO_3200020": "Established", "obo:IAO_0000115": { "@language": "en", "@value": "The closeness of mass to the accepted reference or true value." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/375" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000368", "rdfs:label": { "@language": "en", "@value": "Mass Accuracy" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb382" }, { "@id": "bemo:BEMO_1100014" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb382", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000368" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "https://w3id.org/bemo/profile/BEMO_2000283", "@type": "bemo:BEMO_0000100", "bemo:BEMO_3000007": { "@id": "bemo:BEMO_4000001" }, "bemo:BEMO_3000008": { "@id": "bemo:BEMO_4000007" }, "bemo:BEMO_3000009": { "@id": "bemo:BEMO_4000014" }, "bemo:BEMO_3000010": { "@id": "bemo:BEMO_4000018" }, "bemo:BEMO_3000011": { "@id": "bemo:BEMO_4000021" }, "bemo:BEMO_3100002": "0.1.0", "bemo:BEMO_3100003": { "@language": "en", "@value": "Apply a versioned metric-specific computation protocol consistent with the source definition, criteria, and methods." }, "bemo:BEMO_3100004": "BEMO-Expression-JSON", "bemo:BEMO_3100005": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\"}", "bemo:BEMO_3100006": "evidence_records; 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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.\", \"Evidence Level Where Used\": \"Result / experiment / study / body of evidence, as applicable\", \"Frequency of Use\": \"Established within specialty\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.\", \"Metric\": \"Potency Reproducibility\", \"References or Origin\": \"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\", \"Related Frameworks\": \"OECD; OHAT; FDA Biomarker; EMA E16\", \"Scientific Definition\": \"The degree to which potency reproducibility yields concordant results under the specified repeated-analysis or repeated-measurement conditions.\", \"Scientific Importance (1–10)\": \"10\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Metric-specific continuous, categorical, or ordinal scale\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 356" }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/399", "@type": "prov:Entity", "bemo:BEMO_3100022": 399, "bemo:BEMO_3100023": "e6b0ec1b803bb2c7cb8becab175dbb88ab91c9d8ccd3f713a814c836846ea547", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"All experimental, computational, clinical, and omics studies\", \"Category\": \"Reproducibility and Replication\", \"Closely Related Metrics\": \"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.\", \"Evidence Level Where Used\": \"Result / experiment / study / body of evidence, as applicable\", \"Frequency of Use\": \"Established within specialty\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Mature\", \"Measurement Criteria\": \"Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.\", \"Metric\": \"Direct Replication Success\", \"References or Origin\": \"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\", \"Related Frameworks\": \"PRISMA; CONSORT; MIAME; MINSEQE; MIAPE; ARRIVE 2.0\", \"Scientific Definition\": \"A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of direct replication success.\", \"Scientific Importance (1–10)\": \"10\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Metric-specific continuous, categorical, or ordinal scale\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 399" }, { "@id": "bemo:BEMO_2000234", "@type": "owl:Class", "bemo:BEMO_3100001": "BEMO:2000234", "bemo:BEMO_3100022": 241, "bemo:BEMO_3100023": "103d1dc365ad36d3caee0208333084352e814015d8cdbebbb9964106d3315f21", "bemo:BEMO_3100024": 9, "bemo:BEMO_3200002": { "@language": "en", "@value": "Assesses variant classification stability using evidence appropriate to genetics and variant evidence, distinguishing random uncertainty from systematic error." }, "bemo:BEMO_3200003": { "@language": "en", "@value": "Material weakness in variant classification stability can change the direction, magnitude, certainty, or biological interpretation of the research conclusion." }, "bemo:BEMO_3200004": { "@language": "en", "@value": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "ClinGen/ACMG evidence scoring; pedigree analysis; population databases; case-control data; functional assays; expert-panel review." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Result / experiment / study / body of evidence, as applicable" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "Mendelian disease, cancer genetics, association, segregation, and functional studies" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "ClinGen; ACMG AMP; STREGA; Gene Ontology" }, "bemo:BEMO_3200011": "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/", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000234" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000216" }, { "@id": "bemo:BEMO_2000222" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Established within specialty", "bemo:BEMO_3200020": "Established", "obo:IAO_0000115": { "@language": "en", "@value": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of variant classification stability." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/241" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000234", "rdfs:label": { "@language": "en", "@value": "Variant Classification Stability" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb262" }, { "@id": "bemo:BEMO_1100009" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb262", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000234" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/140", "@type": "prov:Entity", "bemo:BEMO_3100022": 140, "bemo:BEMO_3100023": "74d83029c18dff3247c8fb9baae1d6aba52c9b7328d218dd0210458cbd5ad7d5", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Diagnostic accuracy, screening, prognostic-factor, and prediction-model studies\", \"Category\": \"Diagnostic and Prognostic Evidence\", \"Closely Related Metrics\": \"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.\", \"Evidence Level Where Used\": \"Result / experiment / study / body of evidence, as applicable\", \"Frequency of Use\": \"Common within specialty\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.\", \"Metric\": \"Reclassification Improvement\", \"References or Origin\": \"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/\", \"Related Frameworks\": \"QUADAS-2; STARD; TRIPOD; REMARK\", \"Scientific Definition\": \"A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of reclassification improvement.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Metric-specific continuous, categorical, or ordinal scale\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 140" }, { "@id": "bemo:BEMO_2000033", "@type": "owl:Class", "bemo:BEMO_3100001": "BEMO:2000033", "bemo:BEMO_3100022": 40, "bemo:BEMO_3100023": "d54499df144e3534026302c035690746b731c0abf25107f5fccdd8bada0bd79a", "bemo:BEMO_3100024": 8, "bemo:BEMO_3200002": { "@language": "en", "@value": "Assesses biomarker-outcome association strength using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error." }, "bemo:BEMO_3200003": { "@language": "en", "@value": "Material weakness in biomarker-outcome association strength can change the direction, magnitude, certainty, or biological interpretation of the research conclusion." }, "bemo:BEMO_3200004": { "@language": "en", "@value": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Result / experiment / study / body of evidence, as applicable" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "Biomarker development, qualification, endpoint and surrogate validation studies" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "FDA Biomarker; BEST; EMA E16; REMARK" }, "bemo:BEMO_3200011": "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/", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000033" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000028" }, { "@id": "bemo:BEMO_2000034" }, { "@id": "bemo:BEMO_2000037" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Common within specialty", "bemo:BEMO_3200020": "Established", "obo:IAO_0000115": { "@language": "en", "@value": "The magnitude and credibility of independent evidence supporting biomarker-outcome association." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/40" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000033", "rdfs:label": { "@language": "en", "@value": "Biomarker-Outcome Association Strength" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb21" }, { "@id": "bemo:BEMO_1100002" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb21", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000033" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "bemo:BEMO_2000213", "@type": "owl:Class", "bemo:BEMO_3100001": "BEMO:2000213", "bemo:BEMO_3100022": 220, "bemo:BEMO_3100023": "e9e681d8a3c5b4ca82348a6cd8fe70f3f48bd8351d482c3aa492a6712873c3db", "bemo:BEMO_3100024": 8, "bemo:BEMO_3200002": { "@language": "en", "@value": "Assesses case-level evidence strength using evidence appropriate to genetics and variant evidence, distinguishing random uncertainty from systematic error." }, "bemo:BEMO_3200003": { "@language": "en", "@value": "Material weakness in case-level evidence strength can change the direction, magnitude, certainty, or biological interpretation of the research conclusion." }, "bemo:BEMO_3200004": { "@language": "en", "@value": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Result / experiment / study / body of evidence, as applicable" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "Mendelian disease, cancer genetics, association, segregation, and functional studies" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "ClinGen; ACMG AMP; STREGA; Gene Ontology" }, "bemo:BEMO_3200011": "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/", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000213" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000211" }, { "@id": "bemo:BEMO_2000212" }, { "@id": "bemo:BEMO_2000220" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Established within specialty", "bemo:BEMO_3200020": "Established", "obo:IAO_0000115": { "@language": "en", "@value": "The magnitude and credibility of independent evidence supporting case-level evidence." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/220" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000213", "rdfs:label": { "@language": "en", "@value": "Case-Level Evidence Strength" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb243" }, { "@id": "bemo:BEMO_1100009" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb243", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000213" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "https://w3id.org/bemo/profile/BEMO_2000246", "@type": "bemo:BEMO_0000100", "bemo:BEMO_3000007": { "@id": "bemo:BEMO_4000004" }, "bemo:BEMO_3000008": { "@id": "bemo:BEMO_4000008" }, "bemo:BEMO_3000009": { "@id": "bemo:BEMO_4000017" }, "bemo:BEMO_3000010": { "@id": "bemo:BEMO_4000019" }, "bemo:BEMO_3000011": { "@id": "bemo:BEMO_4000021" }, "bemo:BEMO_3100002": "0.1.0", "bemo:BEMO_3100003": { "@language": "en", "@value": "value = numerator / denominator, with denominator > 0" }, "bemo:BEMO_3100004": "BEMO-Expression-JSON", "bemo:BEMO_3100005": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}", "bemo:BEMO_3100006": "numerator; denominator; operational_definition; assessment_context", "bemo:BEMO_3100007": "weight; stratum; confidence_level", "bemo:BEMO_3100008": "xsd:decimal", "bemo:BEMO_3100009": "Proportion or percentage (0–1 or 0–100%)", "bemo:BEMO_3100010": { "@type": "xsd:decimal", "@value": "0.0" }, "bemo:BEMO_3100011": { "@type": "xsd:decimal", "@value": "1.0" }, "bemo:BEMO_3100013": { "@language": "en", "@value": "Not specified in source; must be defined and versioned before composite use." }, "bemo:BEMO_3100014": { "@language": "en", "@value": "None by default; any normalization must be justified, versioned, and validated." }, "bemo:BEMO_3100015": { "@language": "en", "@value": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material." }, "bemo:BEMO_3100016": true, "bemo:BEMO_3100017": { "@language": "en", "@value": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable." }, "bemo:BEMO_3100018": true, "bemo:BEMO_3100019": { "@language": "en", "@value": "Prespecify, justify, version, and sensitivity-test thresholds; 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appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Result / experiment / study / body of evidence, as applicable" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "Biomarker development, qualification, endpoint and surrogate validation studies" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "FDA Biomarker; 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HUPO PSI; Metabolomics Standards" }, "bemo:BEMO_3200011": "https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000378" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000375" }, { "@id": "bemo:BEMO_2000380" }, { "@id": "bemo:BEMO_2000384" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Established within specialty", "bemo:BEMO_3200020": "Established", "obo:IAO_0000115": { "@language": "en", "@value": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of protein inference reliability." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/385" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000378", "rdfs:label": { "@language": "en", "@value": "Protein Inference Reliability" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb390" }, { "@id": "bemo:BEMO_1100014" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb390", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000378" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/85", "@type": "prov:Entity", "bemo:BEMO_3100022": 85, "bemo:BEMO_3100023": "98ac509f170b3163d862e8e08cc16dad8b915df5508f4e7394a8627d881f7350", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"All studies using human or animal biospecimens\", \"Category\": \"Biospecimen and Preanalytical Quality\", \"Closely Related Metrics\": \"Icterus Interference; 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appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Result / experiment / study / body of evidence, as applicable" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "OECD; 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ISO 15189; REMARK\", \"Scientific Definition\": \"A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of chain-of-custody integrity.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Ordinal rubric, domain judgment, or normalized score\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 69" }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/357", "@type": "prov:Entity", "bemo:BEMO_3100022": 357, "bemo:BEMO_3100023": "5025e34702ce03c8ed7e7aa3ed95dd9bde6bac1786183651ce608b34ffcc6a28", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Pharmacology, pharmacokinetics, toxicology, safety and mode-of-action studies\", \"Category\": \"Pharmacology and Toxicology\", \"Closely Related Metrics\": \"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.\", \"Evidence Level Where Used\": \"Result / experiment / study / body of evidence, as applicable\", \"Frequency of Use\": \"Established within specialty\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.\", \"Metric\": \"Receptor Occupancy Evidence\", \"References or Origin\": \"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\", \"Related Frameworks\": \"OECD; OHAT; FDA Biomarker; EMA E16\", \"Scientific Definition\": \"A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of receptor occupancy evidence.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Metric-specific continuous, categorical, or ordinal scale\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 357" }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/93", "@type": "prov:Entity", "bemo:BEMO_3100022": 93, "bemo:BEMO_3100023": "a6559bfe5ff78dd7455ed538b35cec6508c7c5507441bc614a71e2140188258e", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Randomized and observational etiologic studies, natural experiments, target-trial emulations\", \"Category\": \"Causal Inference\", \"Closely Related Metrics\": \"Confounding Risk; 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direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Result / experiment / study / body of evidence, as applicable" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI" }, "bemo:BEMO_3200011": "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", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000486" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000465" }, { "@id": "bemo:BEMO_2000472" }, { "@id": "bemo:BEMO_2000483" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Common", "bemo:BEMO_3200020": "Established", "obo:IAO_0000115": { "@language": "en", "@value": "The probability or degree that selective outcome reporting introduces systematic distortion into a biomedical estimate or conclusion." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/493" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000486", "rdfs:label": { "@language": "en", "@value": "Selective Outcome Reporting Risk" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb486" }, { "@id": "bemo:BEMO_1100018" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb486", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000486" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "https://w3id.org/bemo/profile/BEMO_2000251", "@type": "bemo:BEMO_0000100", "bemo:BEMO_3000007": { "@id": "bemo:BEMO_4000002" }, "bemo:BEMO_3000008": { "@id": "bemo:BEMO_4000011" }, "bemo:BEMO_3000009": { "@id": "bemo:BEMO_4000016" }, "bemo:BEMO_3000010": { "@id": "bemo:BEMO_4000018" }, "bemo:BEMO_3000011": { "@id": "bemo:BEMO_4000021" }, "bemo:BEMO_3100002": "0.1.0", "bemo:BEMO_3100003": { "@language": "en", "@value": "Apply a versioned, prespecified domain rubric or validated normalized scoring model." }, "bemo:BEMO_3100004": "BEMO-Expression-JSON", "bemo:BEMO_3100005": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"external_protocol\",\"protocolRef\":\"REQUIRED\",\"allowed_outputs\":[\"ordinal_category\",\"normalized_score\"]}", "bemo:BEMO_3100006": "evidence_records; 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do not derive and evaluate on the same data without correction." }, "bemo:BEMO_3100020": { "@language": "en", "@value": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable." }, "bemo:BEMO_3100021": { "@language": "en", "@value": "Required for normalized scores; inter-rater reliability required for human rubrics." }, "bemo:BEMO_3100030": { "@language": "en", "@value": "Source maturity: Established; BEMO computation profile requires independent validation." }, "dcterms:subject": { "@id": "bemo:BEMO_2000251" }, "prov:wasDerivedFrom": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/258" }, "rdfs:label": { "@language": "en", "@value": "Computation profile for Normalization Adequacy" } }, { "@id": "bemo:BEMO_2000041", "@type": "owl:Class", "bemo:BEMO_3100001": "BEMO:2000041", "bemo:BEMO_3100022": 48, "bemo:BEMO_3100023": "c0e22c7d45b8b17a4c9f1de5c7c7bb4e085d98eb667da8d43e452ea31955900b", "bemo:BEMO_3100024": 10, "bemo:BEMO_3200002": { "@language": "en", "@value": "Assesses discriminant validity using evidence appropriate to biomarker and endpoint validation, distinguishing random uncertainty from systematic error." }, "bemo:BEMO_3200003": { "@language": "en", "@value": "Material weakness in discriminant validity can change the direction, magnitude, certainty, or biological interpretation of the research conclusion." }, "bemo:BEMO_3200004": { "@language": "en", "@value": "Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Result / experiment / study / body of evidence, as applicable" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "Biomarker development, qualification, endpoint and surrogate validation studies" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "FDA Biomarker; 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appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Dataset / model / pathway / network / evidence body" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "Integrated omics, networks, pathways, mechanistic and dynamic systems models" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "Gene Ontology; Reactome; UniProt; GA4GH" }, "bemo:BEMO_3200011": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000324" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000307" }, { "@id": "bemo:BEMO_2000309" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Established within specialty", "bemo:BEMO_3200020": "Established", "obo:IAO_0000115": { "@language": "en", "@value": "The closeness of perturbation prediction to the accepted reference or true value." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/331" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000324", "rdfs:label": { "@language": "en", "@value": "Perturbation Prediction Accuracy" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb342" }, { "@id": "bemo:BEMO_1100012" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb342", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000324" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "bemo:BEMO_0000100", "@type": "owl:Class", "bemo:BEMO_3200016": "Candidate", "obo:IAO_0000115": { "@language": "en", "@value": "An information content entity specifying inputs, outputs, formula status, uncertainty, thresholds, missing-data policy, and validation requirements for computing a metric." }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:0000100", "rdfs:label": { "@language": "en", "@value": "metric computation specification" }, "rdfs:subClassOf": { "@id": "obo:IAO_0000030" } }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/492", "@type": "prov:Entity", "bemo:BEMO_3100022": 492, "bemo:BEMO_3100023": "8438f239c984919f366a44747e2e32efd683c0e45e3f7af6c269801f1d6694c8", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies\", \"Category\": \"Study Design and Internal Validity\", \"Closely Related Metrics\": \"Allocation Concealment; 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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.\", \"Evidence Level Where Used\": \"Body of evidence / synthesis / outcome\", \"Frequency of Use\": \"Common\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.\", \"Metric\": \"Selective Nonreporting Risk\", \"References or Origin\": \"https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/\", \"Related Frameworks\": \"GRADE; PRISMA; AMSTAR 2; RoB\", \"Scientific Definition\": \"The probability or degree that selective nonreporting introduces systematic distortion into a biomedical estimate or conclusion.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Ordinal risk rating or quantitative percentage/probability; lower is generally better\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 170" }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/193", "@type": "prov:Entity", "bemo:BEMO_3100022": 193, "bemo:BEMO_3100023": "67d1bc84f2c2d0324ee734ed3d2df1c72cd4820b21290b5a8b136d75863a4866", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"In vitro, ex vivo, organoid, animal, and preclinical experiments\", \"Category\": \"Experimental Biology and Animal Research\", \"Closely Related Metrics\": \"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.\", \"Evidence Level Where Used\": \"Result / experiment / study / body of evidence, as applicable\", \"Frequency of Use\": \"Established within specialty\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.\", \"Metric\": \"Sex as a Biological Variable Adequacy\", \"References or Origin\": \"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\", \"Related Frameworks\": \"ARRIVE 2.0; 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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.\", \"Evidence Level Where Used\": \"Body of evidence / synthesis / outcome\", \"Frequency of Use\": \"Common\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds.\", \"Metric\": \"Cumulative Evidence Stability\", \"References or Origin\": \"https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/\", \"Related Frameworks\": \"GRADE; PRISMA; AMSTAR 2; RoB\", \"Scientific Definition\": \"A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of cumulative evidence stability.\", \"Scientific Importance (1–10)\": \"9\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Metric-specific continuous, categorical, or ordinal scale\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 148" }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/389", "@type": "prov:Entity", "bemo:BEMO_3100022": 389, "bemo:BEMO_3100023": "6e5af7c1fffa7603da0abd7518a670fd09cade5fe3e47c8417886f91e6b4e07a", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies\", \"Category\": \"Proteomics and Metabolomics\", \"Closely Related Metrics\": \"Sequence Coverage; 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MINSEQE; STROBE-ME; GA4GH; HCA" }, "bemo:BEMO_3200011": "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/", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000245" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000242" }, { "@id": "bemo:BEMO_2000249" }, { "@id": "bemo:BEMO_2000253" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Established within specialty", "bemo:BEMO_3200020": "Established", "obo:IAO_0000115": { "@language": "en", "@value": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of duplicate read burden." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/252" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000245", "rdfs:label": { "@language": "en", "@value": "Duplicate Read Burden" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb271" }, { "@id": "bemo:BEMO_1100010" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb271", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000245" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/249", "@type": "prov:Entity", "bemo:BEMO_3100022": 249, "bemo:BEMO_3100023": "fc0cd98bc92235d469bf2bc025f0d327d8170dfb4df97b973710a8d887eff3f4", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies\", \"Category\": \"Genomics and Transcriptomics\", \"Closely Related Metrics\": \"Library Complexity; 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STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI\", \"Scientific Definition\": \"The extent to which all scientifically necessary components of follow-up are present, documented, and evaluable.\", \"Scientific Importance (1–10)\": \"9\", \"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%)\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 485" }, { "@id": "bemo:BEMO_2000143", "@type": "owl:Class", "bemo:BEMO_3100001": "BEMO:2000143", "bemo:BEMO_3100022": 150, "bemo:BEMO_3100023": "263bd485141b0cc75ee285fb1989c667b83eb378666886a960ed5bd2a610f232", "bemo:BEMO_3100024": 9, "bemo:BEMO_3200002": { "@language": "en", "@value": "Assesses evidence completeness using evidence appropriate to evidence certainty and synthesis, distinguishing random uncertainty from systematic error." }, "bemo:BEMO_3200003": { "@language": "en", "@value": "Material weakness in evidence completeness can change the direction, magnitude, certainty, or biological interpretation of the research conclusion." }, "bemo:BEMO_3200004": { "@language": "en", "@value": "Required elements present; traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Body of evidence / synthesis / outcome" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "Systematic reviews, meta-analyses, evidence profiles, guidelines" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "GRADE; PRISMA; AMSTAR 2; RoB" }, "bemo:BEMO_3200011": "https://www.gradeworkinggroup.org/ | https://www.prisma-statement.org/prisma-2020-checklist | https://www.bmj.com/content/358/bmj.j4008 | https://www.riskofbias.info/", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000143" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000147" }, { "@id": "bemo:BEMO_2000149" }, { "@id": "bemo:BEMO_2000155" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Common", "bemo:BEMO_3200020": "Established", "obo:IAO_0000115": { "@language": "en", "@value": "The extent to which all scientifically necessary components of evidence are present, documented, and evaluable." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/150" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000143", "rdfs:label": { "@language": "en", "@value": "Evidence Completeness" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb182" }, { "@id": "bemo:BEMO_1100006" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb182", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000143" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/287", "@type": "prov:Entity", "bemo:BEMO_3100022": 287, "bemo:BEMO_3100023": "41309e5f36c397d08d76621c273137352b099c93484f2a2eca025bcf85ccffdc", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies\", \"Category\": \"Measurement and Assay Analytical Validity\", \"Closely Related Metrics\": \"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.\", \"Evidence Level Where Used\": \"Specimen / assay / run / laboratory / study\", \"Frequency of Use\": \"Common within specialty\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.\", \"Metric\": \"Dynamic Range\", \"References or Origin\": \"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/\", \"Related Frameworks\": \"FDA Biomarker; CLSI; ISO 15189; MIQE\", \"Scientific Definition\": \"A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of dynamic range.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Method- and analyte-specific physical units\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 287" }, { "@id": "https://w3id.org/bemo/alignment/OBI", "@type": "prov:Entity", "dcterms:source": { "@id": "obo:obi.owl" } }, { "@id": "bemo:BEMO_2000405", "@type": "owl:Class", "bemo:BEMO_3100001": "BEMO:2000405", "bemo:BEMO_3100022": 412, "bemo:BEMO_3100023": "60121a2998efa943018d3ff7dd4130d4332ee279da0e8111b650ea175e9dacce", "bemo:BEMO_3100024": 10, "bemo:BEMO_3200002": { "@language": "en", "@value": "Assesses result reproducibility using evidence appropriate to reproducibility and replication, distinguishing random uncertainty from systematic error." }, "bemo:BEMO_3200003": { "@language": "en", "@value": "Material weakness in result reproducibility can change the direction, magnitude, certainty, or biological interpretation of the research conclusion." }, "bemo:BEMO_3200004": { "@language": "en", "@value": "Independent repeats; between-run/site/analyst variability; concordance of effect direction and magnitude; predefined reproducibility thresholds." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Result / experiment / study / body of evidence, as applicable" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "All experimental, computational, clinical, and omics studies" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "PRISMA; CONSORT; MIAME; MINSEQE; MIAPE; ARRIVE 2.0" }, "bemo:BEMO_3200011": "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", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000405" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000395" }, { "@id": "bemo:BEMO_2000399" }, { "@id": "bemo:BEMO_2000403" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Established within specialty", "bemo:BEMO_3200020": "Established", "obo:IAO_0000115": { "@language": "en", "@value": "The degree to which result reproducibility yields concordant results under the specified repeated-analysis or repeated-measurement conditions." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/412" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000405", "rdfs:label": { "@language": "en", "@value": "Result Reproducibility" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb415" }, { "@id": "bemo:BEMO_1100015" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb415", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000405" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/479", "@type": "prov:Entity", "bemo:BEMO_3100022": 479, "bemo:BEMO_3100023": "eed78db6e72161c41f0a51c8bc55e5d20b0d6675373ef1a7bf65b4c5b0dc75c0", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies\", \"Category\": \"Study Design and Internal Validity\", \"Closely Related Metrics\": \"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.\", \"Evidence Level Where Used\": \"Result / experiment / study / body of evidence, as applicable\", \"Frequency of Use\": \"Common\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Prespecified signaling questions; direction and likely magnitude of distortion; domain-level and overall judgment; sensitivity to plausible bias.\", \"Metric\": \"Contamination Risk\", \"References or Origin\": \"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\", \"Related Frameworks\": \"CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI\", \"Scientific Definition\": \"The probability or degree that contamination introduces systematic distortion into a biomedical estimate or conclusion.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Ordinal risk rating or quantitative percentage/probability; lower is generally better\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 479" }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/70", "@type": "prov:Entity", "bemo:BEMO_3100022": 70, "bemo:BEMO_3100023": "450f9e94b009036abe7a13fe3055116e7c4959857a7291ed7e337a746d7bf722", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"All studies using human or animal biospecimens\", \"Category\": \"Biospecimen and Preanalytical Quality\", \"Closely Related Metrics\": \"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.\", \"Evidence Level Where Used\": \"Specimen / assay / run / laboratory / study\", \"Frequency of Use\": \"Established within specialty\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.\", \"Metric\": \"Cold Ischemia Control\", \"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/\", \"Related Frameworks\": \"BRISQ; ISO 15189; REMARK\", \"Scientific Definition\": \"A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of cold ischemia control.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Metric-specific continuous, categorical, or ordinal scale\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 70" }, { "@id": "bemo:BEMO_4000005", "@type": [ "owl:NamedIndividual", "bemo:BEMO_0000400" ], "obo:IAO_0000115": { "@language": "en", "@value": "Controlled BEMO ScaleType value: RatioScale." }, "oboInOwl:id": "BEMO:4000005", "rdfs:label": { "@language": "en", "@value": "Ratio Scale" }, "skos:notation": "RatioScale" }, { "@id": "bemo:BEMO_3100026", "@type": "owl:DatatypeProperty", "obo:IAO_0000115": { "@language": "en", "@value": "Numeric metric assessment value." }, "oboInOwl:id": "BEMO:3100026", "rdfs:label": { "@language": "en", "@value": "numeric metric value" } }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/298", "@type": "prov:Entity", "bemo:BEMO_3100022": 298, "bemo:BEMO_3100023": "ae9e50b8f8857543ecb1eb315c23fc88dd3a028cfd40ee4377e1039431544ca0", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Laboratory-developed tests, molecular assays, imaging, pathology, biomarker studies\", \"Category\": \"Measurement and Assay Analytical Validity\", \"Closely Related Metrics\": \"Instrument Drift; 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CLSI; ISO 15189; MIQE\", \"Scientific Definition\": \"A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of operator variability.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Metric-specific continuous, categorical, or ordinal scale\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 298" }, { "@id": "bemo:BEMO_2000222", "@type": "owl:Class", "bemo:BEMO_3100001": "BEMO:2000222", "bemo:BEMO_3100022": 229, "bemo:BEMO_3100023": "baeee8e900a9ffef8f3ddd054b3a12f2233d89fc626f852fd31efc4b84b81685", "bemo:BEMO_3100024": 8, "bemo:BEMO_3200002": { "@language": "en", "@value": "Assesses genotype–phenotype concordance using evidence appropriate to genetics and variant evidence, distinguishing random uncertainty from systematic error." }, "bemo:BEMO_3200003": { "@language": "en", "@value": "Material weakness in genotype–phenotype concordance can change the direction, magnitude, certainty, or biological interpretation of the research conclusion." }, "bemo:BEMO_3200004": { "@language": "en", "@value": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Read- and variant-level quality-control summaries; replicate concordance; orthogonal confirmation; benchmarking against reference materials." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Result / experiment / study / body of evidence, as applicable" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "Mendelian disease, cancer genetics, association, segregation, and functional studies" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "ClinGen; 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appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Result / experiment / study / body of evidence, as applicable" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "MIAME; MINSEQE; STROBE-ME; GA4GH; HCA" }, "bemo:BEMO_3200011": "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/", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000241" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000243" }, { "@id": "bemo:BEMO_2000261" }, { "@id": "bemo:BEMO_2000263" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Established within specialty", "bemo:BEMO_3200020": "Established", "obo:IAO_0000115": { "@language": "en", "@value": "The justified degree of certainty assigned to cell-type annotation given the quantity, quality, consistency, and limitations of supporting evidence." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/248" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000241", "rdfs:label": { "@language": "en", "@value": "Cell-Type Annotation Confidence" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb268" }, { "@id": "bemo:BEMO_1100010" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb268", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000241" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "bemo:BEMO_2000308", "@type": "owl:Class", "bemo:BEMO_3100001": "BEMO:2000308", "bemo:BEMO_3100022": 315, "bemo:BEMO_3100023": "81ae3d3ac205c8d1258be22f4b5818a5c36df354b19605060eb458cfdfef682e", "bemo:BEMO_3100024": 8, "bemo:BEMO_3200002": { "@language": "en", "@value": "Assesses entity resolution accuracy using evidence appropriate to multi-omics and systems biology, distinguishing random uncertainty from systematic error." }, "bemo:BEMO_3200003": { "@language": "en", "@value": "Material weakness in entity resolution accuracy can change the direction, magnitude, certainty, or biological interpretation of the research conclusion." }, "bemo:BEMO_3200004": { "@language": "en", "@value": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Dataset / model / pathway / network / evidence body" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "Integrated omics, networks, pathways, mechanistic and dynamic systems models" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "Gene Ontology; Reactome; UniProt; GA4GH" }, "bemo:BEMO_3200011": "https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000308" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000311" }, { "@id": "bemo:BEMO_2000318" }, { "@id": "bemo:BEMO_2000326" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Established within specialty", "bemo:BEMO_3200020": "Established", "obo:IAO_0000115": { "@language": "en", "@value": "The closeness of entity resolution to the accepted reference or true value." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/315" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000308", "rdfs:label": { "@language": "en", "@value": "Entity Resolution Accuracy" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb326" }, { "@id": "bemo:BEMO_1100012" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb326", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000308" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "https://w3id.org/bemo/profile/BEMO_2000270", "@type": "bemo:BEMO_0000100", "bemo:BEMO_3000007": { "@id": "bemo:BEMO_4000004" }, "bemo:BEMO_3000008": { "@id": "bemo:BEMO_4000008" }, "bemo:BEMO_3000009": { "@id": "bemo:BEMO_4000017" }, "bemo:BEMO_3000010": { "@id": "bemo:BEMO_4000019" }, "bemo:BEMO_3000011": { "@id": "bemo:BEMO_4000021" }, "bemo:BEMO_3100002": "0.1.0", "bemo:BEMO_3100003": { "@language": "en", "@value": "value = numerator / denominator, with denominator > 0" }, "bemo:BEMO_3100004": "BEMO-Expression-JSON", "bemo:BEMO_3100005": "{\"language\":\"BEMO-Expression-JSON\",\"operator\":\"divide\",\"arguments\":[\"numerator\",\"denominator\"],\"constraints\":[\"denominator > 0\"]}", "bemo:BEMO_3100006": "numerator; denominator; operational_definition; assessment_context", "bemo:BEMO_3100007": "weight; stratum; confidence_level", "bemo:BEMO_3100008": "xsd:decimal", "bemo:BEMO_3100009": "Proportion or percentage (0–1 or 0–100%)", "bemo:BEMO_3100010": { "@type": "xsd:decimal", "@value": "0.0" }, "bemo:BEMO_3100011": { "@type": "xsd:decimal", "@value": "1.0" }, "bemo:BEMO_3100013": { "@language": "en", "@value": "Not specified in source; must be defined and versioned before composite use." }, "bemo:BEMO_3100014": { "@language": "en", "@value": "None by default; any normalization must be justified, versioned, and validated." }, "bemo:BEMO_3100015": { "@language": "en", "@value": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material." }, "bemo:BEMO_3100016": true, "bemo:BEMO_3100017": { "@language": "en", "@value": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable." }, "bemo:BEMO_3100018": true, "bemo:BEMO_3100019": { "@language": "en", "@value": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction." }, "bemo:BEMO_3100020": { "@language": "en", "@value": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable." }, "bemo:BEMO_3100021": { "@language": "en", "@value": "As applicable; required when interpreted probabilistically." }, "bemo:BEMO_3100030": { "@language": "en", "@value": "Source maturity: Mature; BEMO computation profile requires independent validation." }, "dcterms:subject": { "@id": "bemo:BEMO_2000270" }, "prov:wasDerivedFrom": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/277" }, "rdfs:label": { "@language": "en", "@value": "Computation profile for Analytical Sensitivity" } }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/115", "@type": "prov:Entity", "bemo:BEMO_3100022": 115, "bemo:BEMO_3100023": "f46690f0cea7611ea5bb0e9a0e5c1b90d25ecad9c8f28f3083cc2a71b53ce7f0", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Randomized and observational etiologic studies, natural experiments, target-trial emulations\", \"Category\": \"Causal Inference\", \"Closely Related Metrics\": \"Collider Bias Risk; 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appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Result / experiment / study / body of evidence, as applicable" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "Biomarker development, qualification, endpoint and surrogate validation studies" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "FDA Biomarker; 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STROBE; TRIPOD; REMARK; ICH E9" }, "bemo:BEMO_3200011": "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", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000434" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000432" }, { "@id": "bemo:BEMO_2000436" }, { "@id": "bemo:BEMO_2000442" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Common", "bemo:BEMO_3200020": "Established", "obo:IAO_0000115": { "@language": "en", "@value": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of clinical relevance of effect." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/441" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000434", "rdfs:label": { "@language": "en", "@value": "Clinical Relevance of Effect" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb440" }, { "@id": "bemo:BEMO_1100017" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb440", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000434" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/178", "@type": "prov:Entity", "bemo:BEMO_3100022": 178, "bemo:BEMO_3100023": "74976e4cf57f53c444f4721c04fc26fb7298cad4ac743db45feeb9a0be34587a", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"In vitro, ex vivo, organoid, animal, and preclinical experiments\", \"Category\": \"Experimental Biology and Animal Research\", \"Closely Related Metrics\": \"Experimental Unit Validity; 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appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Result / experiment / study / body of evidence, as applicable" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "Biomarker development, qualification, endpoint and surrogate validation studies" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "FDA Biomarker; BEST; EMA E16; REMARK" }, "bemo:BEMO_3200011": "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/", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000042" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000043" }, { "@id": "bemo:BEMO_2000047" }, { "@id": "bemo:BEMO_2000049" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Common within specialty", "bemo:BEMO_3200020": "Established", "obo:IAO_0000115": { "@language": "en", "@value": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of endpoint reliability." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/49" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000042", "rdfs:label": { "@language": "en", "@value": "Endpoint Reliability" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb91" }, { "@id": "bemo:BEMO_1100002" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb91", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000042" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "bemo:BEMO_2000177", "@type": "owl:Class", "bemo:BEMO_3100001": "BEMO:2000177", "bemo:BEMO_3100022": 184, "bemo:BEMO_3100023": "3f6791503c2895971802b5fb5573311999fc32cde51839dc771c56e4855ceb83", "bemo:BEMO_3100024": 8, "bemo:BEMO_3200002": { "@language": "en", "@value": "Assesses genetic background control using evidence appropriate to experimental biology and animal research, distinguishing random uncertainty from systematic error." }, "bemo:BEMO_3200003": { "@language": "en", "@value": "Material weakness in genetic background control can change the direction, magnitude, certainty, or biological interpretation of the research conclusion." }, "bemo:BEMO_3200004": { "@language": "en", "@value": "Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Result / experiment / study / body of evidence, as applicable" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "In vitro, ex vivo, organoid, animal, and preclinical experiments" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "ARRIVE 2.0; SYRCLE; OECD" }, "bemo:BEMO_3200011": "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", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000177" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000166" }, { "@id": "bemo:BEMO_2000173" }, { "@id": "bemo:BEMO_2000178" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Established within specialty", "bemo:BEMO_3200020": "Established", "obo:IAO_0000115": { "@language": "en", "@value": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of genetic background control." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/184" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000177", "rdfs:label": { "@language": "en", "@value": "Genetic Background Control" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb211" }, { "@id": "bemo:BEMO_1100007" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb211", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000177" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/164", "@type": "prov:Entity", "bemo:BEMO_3100022": 164, "bemo:BEMO_3100023": "1349313eaf86ad90454f8dbf26aa9cb5389132fc9ac2e44b703024851df5136c", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Systematic reviews, meta-analyses, evidence profiles, guidelines\", \"Category\": \"Evidence Certainty and Synthesis\", \"Closely Related Metrics\": \"Cumulative Evidence Stability; 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PRISMA; AMSTAR 2; RoB\", \"Scientific Definition\": \"The extent to which information size is sufficient and fit for the stated biomedical inference.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Ordinal rubric, domain judgment, or normalized score\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 164" }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/316", "@type": "prov:Entity", "bemo:BEMO_3100022": 316, "bemo:BEMO_3100023": "f8d3b19efd68e0150e437c71bac90ab2bb80f33877b4a0e74bc52542a0fd3c26", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Integrated omics, networks, pathways, mechanistic and dynamic systems models\", \"Category\": \"Multi-omics and Systems Biology\", \"Closely Related Metrics\": \"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.\", \"Evidence Level Where Used\": \"Dataset / model / pathway / network / evidence body\", \"Frequency of Use\": \"Established within specialty\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.\", \"Metric\": \"Flux-Balance Consistency\", \"References or Origin\": \"https://geneontology.org/docs/guide-go-evidence-codes/ | https://reactome.org/ | https://www.uniprot.org/help/evidences | https://www.ga4gh.org/\", \"Related Frameworks\": \"Gene Ontology; Reactome; UniProt; GA4GH\", \"Scientific Definition\": \"The degree of agreement in flux-balance across measurements, studies, methods, populations, or biological levels.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Metric-specific continuous, categorical, or ordinal scale\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 316" }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/323", "@type": "prov:Entity", "bemo:BEMO_3100022": 323, "bemo:BEMO_3100023": "79eaf0a8e6c6fc3012d48e379c545c17d89aecf6de033d40ae6399ec89441a3b", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Integrated omics, networks, pathways, mechanistic and dynamic systems models\", \"Category\": \"Multi-omics and Systems Biology\", \"Closely Related Metrics\": \"Network Edge Confidence; 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Reactome; UniProt; GA4GH\", \"Scientific Definition\": \"The justified degree of certainty assigned to network node given the quantity, quality, consistency, and limitations of supporting evidence.\", \"Scientific Importance (1–10)\": \"10\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Ordinal rubric, domain judgment, or normalized score\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 323" }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/459", "@type": "prov:Entity", "bemo:BEMO_3100022": 459, "bemo:BEMO_3100023": "5c494db875d0f3ad6860a3bba83e6ac01d9f571b40aa89617a37a42c1c489cab", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"All quantitative biomedical studies\", \"Category\": \"Statistical Validity and Inference\", \"Closely Related Metrics\": \"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.\", \"Evidence Level Where Used\": \"Result / experiment / study / body of evidence, as applicable\", \"Frequency of Use\": \"Common\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; 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traceable provenance; unambiguous definitions; accessible underlying data/materials; documented deviations." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Result / experiment / study / body of evidence, as applicable" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "All experimental, computational, clinical, and omics studies" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "PRISMA; 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appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses." }, "bemo:BEMO_3200005": { "@language": "en", "@value": "Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses." }, "bemo:BEMO_3200006": { "@language": "en", "@value": "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." }, "bemo:BEMO_3200007": { "@language": "en", "@value": "Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence." }, "bemo:BEMO_3200008": { "@language": "en", "@value": "Result / experiment / study / body of evidence, as applicable" }, "bemo:BEMO_3200009": { "@language": "en", "@value": "Molecular, cellular, animal, translational, pharmacologic, and human studies" }, "bemo:BEMO_3200010": { "@language": "en", "@value": "GRADE; FDA Biomarker; ClinGen; OHAT; OECD" }, "bemo:BEMO_3200011": "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", "bemo:BEMO_3200012": { "@id": "https://w3id.org/bemo/profile/BEMO_2000025" }, "bemo:BEMO_3200013": [ { "@id": "bemo:BEMO_2000005" }, { "@id": "bemo:BEMO_2000017" }, { "@id": "bemo:BEMO_2000018" } ], "bemo:BEMO_3200014": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "bemo:BEMO_3200015": "Biomedical Evidence Metrics", "bemo:BEMO_3200016": "Candidate", "bemo:BEMO_3200017": "Pending owner approval; CC BY 4.0 recommended for OBO compatibility.", "bemo:BEMO_3200018": { "@language": "en", "@value": "Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use." }, "bemo:BEMO_3200019": "Established within specialty", "bemo:BEMO_3200020": "Established", "obo:IAO_0000115": { "@language": "en", "@value": "A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of target engagement evidence." }, "obo:IAO_0000119": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/32" }, "oboInOwl:hasOBONamespace": "bemo", "oboInOwl:id": "BEMO:2000025", "rdfs:label": { "@language": "en", "@value": "Target Engagement Evidence" }, "rdfs:subClassOf": [ { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb76" }, { "@id": "bemo:BEMO_1100001" } ] }, { "@id": "_:n3d8500c404224719bd9bf733a5ad4a7cb76", "@type": "owl:Restriction", "owl:hasValue": { "@id": "https://w3id.org/bemo/profile/BEMO_2000025" }, "owl:onProperty": { "@id": "bemo:BEMO_3000001" } }, { "@id": "bemo:BEMO_3100020", "@type": "owl:DatatypeProperty", "obo:IAO_0000115": { "@language": "en", "@value": "Quality-control requirements for computation." }, "oboInOwl:id": "BEMO:3100020", "rdfs:label": { "@language": "en", "@value": "quality control requirements" } }, { "@id": "bemo:BEMO_2000266", "@type": "owl:Class", "bemo:BEMO_3100001": "BEMO:2000266", "bemo:BEMO_3100022": 273, "bemo:BEMO_3100023": "45320c5b96fc37b8148ee2721453c92e6bec79491a4ed2d2f6fedbc2cb99cb01", "bemo:BEMO_3100024": 8, "bemo:BEMO_3200002": { "@language": "en", "@value": "Assesses variant call quality using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error." }, "bemo:BEMO_3200003": { "@language": "en", "@value": "Material weakness in variant call quality can change the direction, magnitude, certainty, or biological interpretation of the research conclusion." }, "bemo:BEMO_3200004": { "@language": "en", "@value": "Prespecified operational definition; 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assessment_context; rubric_or_model_version; evidence_records", "bemo:BEMO_3100007": "weights; thresholds; calibration_dataset", "bemo:BEMO_3100008": "xsd:string_or_decimal", "bemo:BEMO_3100009": "Ordinal risk rating or quantitative percentage/probability; lower is generally better", "bemo:BEMO_3100013": { "@language": "en", "@value": "Not specified in source; must be defined and versioned before composite use." }, "bemo:BEMO_3100014": { "@language": "en", "@value": "None by default; any normalization must be justified, versioned, and validated." }, "bemo:BEMO_3100015": { "@language": "en", "@value": "Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material." }, "bemo:BEMO_3100016": true, "bemo:BEMO_3100017": { "@language": "en", "@value": "Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable." }, "bemo:BEMO_3100018": true, "bemo:BEMO_3100019": { "@language": "en", "@value": "Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction." }, "bemo:BEMO_3100020": { "@language": "en", "@value": "Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable." }, "bemo:BEMO_3100021": { "@language": "en", "@value": "Required for probability outputs; rubric reliability required for ordinal outputs." }, "bemo:BEMO_3100030": { "@language": "en", "@value": "Source maturity: Mature; BEMO computation profile requires independent validation." }, "dcterms:subject": { "@id": "bemo:BEMO_2000087" }, "prov:wasDerivedFrom": { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/94" }, "rdfs:label": { "@language": "en", "@value": "Computation profile for Collider Bias Risk" } }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/180", "@type": "prov:Entity", "bemo:BEMO_3100022": 180, "bemo:BEMO_3100023": "432e96e9d5c02fcda1a353b0ddb2e18d1019ff594f33c248eedfbe337bf31fae", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"In vitro, ex vivo, organoid, animal, and preclinical experiments\", \"Category\": \"Experimental Biology and Animal Research\", \"Closely Related Metrics\": \"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.\", \"Evidence Level Where Used\": \"Result / experiment / study / body of evidence, as applicable\", \"Frequency of Use\": \"Established within specialty\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.\", \"Metric\": \"Environmental Standardization\", \"References or Origin\": \"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\", \"Related Frameworks\": \"ARRIVE 2.0; SYRCLE; OECD\", \"Scientific Definition\": \"A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of environmental standardization.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Metric-specific continuous, categorical, or ordinal scale\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 180" }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/487", "@type": "prov:Entity", "bemo:BEMO_3100022": 487, "bemo:BEMO_3100023": "654f73aad6650cd58d63f5a49ae9e034bfcb22952cbf7a018f652c070e1ba6c1", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Randomized trials, nonrandomized intervention studies, cohort, case-control, cross-sectional studies\", \"Category\": \"Study Design and Internal Validity\", \"Closely Related Metrics\": \"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.\", \"Evidence Level Where Used\": \"Result / experiment / study / body of evidence, as applicable\", \"Frequency of Use\": \"Common\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Mature\", \"Measurement Criteria\": \"Clear intended use or estimand; accepted reference or criterion; prespecified acceptance thresholds; independent validation; performance across relevant conditions.\", \"Metric\": \"Outcome Ascertainment Validity\", \"References or Origin\": \"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\", \"Related Frameworks\": \"CONSORT; STROBE; RoB 2; ROBINS-I; ROBINS-E; NIH Quality Tools; JBI\", \"Scientific Definition\": \"The degree to which outcome ascertainment supports the intended scientific interpretation without material systematic error.\", \"Scientific Importance (1–10)\": \"10\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Ordinal rubric, domain judgment, or normalized score\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 487" }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/373", "@type": "prov:Entity", "bemo:BEMO_3100022": 373, "bemo:BEMO_3100023": "c108ebf1ca903ed7e96063f24ecaf39723dd5e925f97d641601f89fd859897b9", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Mass spectrometry, affinity proteomics, metabolomics, lipidomics studies\", \"Category\": \"Proteomics and Metabolomics\", \"Closely Related Metrics\": \"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.\", \"Evidence Level Where Used\": \"Result / experiment / study / body of evidence, as applicable\", \"Frequency of Use\": \"Established within specialty\", \"Limitations\": \"Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.\", \"Maturity of Metric\": \"Established\", \"Measurement Criteria\": \"Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.\", \"Metric\": \"Ion Suppression Assessment\", \"References or Origin\": \"https://www.psidev.info/miape | https://www.psidev.info/ | https://www.metabolomics-msi.org/\", \"Related Frameworks\": \"MIAPE; HUPO PSI; Metabolomics Standards\", \"Scientific Definition\": \"A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of ion suppression assessment.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Metric-specific continuous, categorical, or ordinal scale\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 373" }, { "@id": "bemo:BEMO_4000029", "@type": [ "owl:NamedIndividual", "bemo:BEMO_0000402" ], "obo:IAO_0000115": { "@language": "en", "@value": "Controlled BEMO ApprovalStatus value: Approved." }, "oboInOwl:id": "BEMO:4000029", "rdfs:label": { "@language": "en", "@value": "Approved" }, "skos:notation": "Approved" }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/446", "@type": "prov:Entity", "bemo:BEMO_3100022": 446, "bemo:BEMO_3100023": "e21896fd55cc8da1ecb273cc15de195832d87a4d4554d2b68b3a9ce060442d84", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"All quantitative biomedical studies\", \"Category\": \"Statistical Validity and Inference\", \"Closely Related Metrics\": \"Estimate Precision; 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STROBE; TRIPOD; REMARK; ICH E9\", \"Scientific Definition\": \"A canonical biomedical evidence metric quantifying the scientific credibility, reliability, relevance, or interpretability of effect magnitude.\", \"Scientific Importance (1–10)\": \"8\", \"Typical Methods of Assessment\": \"Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.\", \"Units or Scale (if applicable)\": \"Metric-specific continuous, categorical, or ordinal scale\", \"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.\"}", "rdfs:label": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 446" }, { "@id": "https://w3id.org/bemo/source/pure_biomedical_evidence_research_metrics_part_2_3_xlsx/row/257", "@type": "prov:Entity", "bemo:BEMO_3100022": 257, "bemo:BEMO_3100023": "aef9eeffa971170a3db3642e806206bdf35806d1d8cc427e16ad9106f7e0207c", "dcterms:source": "Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx", "prov:value": "{\"Applicable Study Types\": \"Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies\", \"Category\": \"Genomics and Transcriptomics\", \"Closely Related Metrics\": \"Genome Coverage Uniformity; 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