A Semantic Model of Genetic Evidence: A Step Toward Bridging the Basic-Science-Clinic Gap

📅 2026-09-03
📈 Citations: 0
Influential: 0
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🤖 AI Summary
本文提出一种语义模型来表示遗传学证据,旨在解决基础科学与临床之间的差距,通过精细分类和结构对齐现有标准,适用于AI辅助的变异解读。
📝 Abstract
Scientific and clinical decision-making depends on evidence from the primary literature, but existing standards for representing that evidence (FHIR Evidence, ECO, SEPIO, and the GA4GH Genomic Knowledge Standards) are oriented toward clinical-trial workflows, evidence codes, or single-variant assertions, and do not capture the fine-grained, domain-specific structure of claims in basic and pre-clinical research. We introduce a semantic model for scientific evidence with three core classes, specialize it for genetics, align it structurally to FHIR Evidence with a SEPIO-anchored credibility decomposition, and attach a compact dimensional vocabulary whose conditional-activation rules are validated by a SHACL schema for the implemented constraints. Using clinical variant interpretation as the driving use case, we evaluate the model through a human-AI annotation pilot over six genetics papers, yielding 28 evidence items and 95 source-anchored assertions, with a workflow that keeps curator-authored reference annotations distinct from AI-drafted annotations. Treating the pilot as a feasibility study rather than a benchmark, we argue that the model is a useful increment toward trustworthy, AI-ready infrastructure for variant interpretation: a reference data model and validation schema for representing genetic evidence.
Problem

Research questions and friction points this paper is trying to address.

Genetic Evidence
Clinical Trial Workflows
Basic Research
Pre-clinical Research
Evidence Representation
Innovation

Methods, ideas, or system contributions that make the work stand out.

semantic model
genetic evidence
FHIR Evidence alignment
SEPIO-anchored credibility decomposition
AI-assisted annotation
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M
Michael Bouzinier
1Harvard University, Cambridge, MA, USA; 2IDEXX Laboratories, Westbrook, ME, USA; 3Forome Association, Newton, MA, USA
D
Dmitry Etin
3Forome Association, Newton, MA, USA; 4Deggendorf Institute of Technology, Germany