Statement & Evidence composition — worked example

va-spec-source.yaml

The same structure as the class diagram, filled in with illustrative example data for a variant pathogenicity assessment. Field names are the same; values here are example data, not type declarations.

TU
«abstract»
Proposition
subject: "HRAS:c.173C>T"
predicate: "is causal for"
object: "Costello Syndrome"
proposition
1..1
TU
Method
name: "ACMG/AMP Guidelines 2015"
methodType: "ACMG guidelines"
specifiedBy
0..1
TU
Statement
direction: "supports"
strength: "high confidence"
score: 0.95
classification: "pathogenic"
hasEvidence: (omitted)
classification is typically translatable with the direction/strength/score tuple of values. Here evidence is organized into an Evidence Line (below); a Statement may also cite it directly via hasEvidence.
contributions
0..m
TU
Contribution
contributor: "Jane Doe, MD"
activityType: "curation"
date: 2024-03-15
reportedIn
0..m
TU
Document
title: "ClinVar SCV0012345"
urls: "clinvar.nih.gov"
hasEvidenceLines 0..m
TU
EvidenceLine
targetProposition: (omitted)
directionOfEvidenceProvided: "supports"
strengthOfEvidenceProvided: "moderate"
evidenceOutcome: "contributing"
targetProposition usually omitted — inherits the parent Statement's claim unless arguing a narrower point. A non‑contributing Evidence Line (noted but not swaying the parent's outcome) has directionOfEvidenceProvided: neutral, with strengthOfEvidenceProvided marking it as additional evidence.
hasEvidenceItems 0..m
additional roles «abstract» = open base class TU Trial Use D Draft