Add biological attribute class for OBA support#1663
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kevinschaper wants to merge 1 commit intomasterfrom
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Add biological attribute class for OBA support#1663kevinschaper wants to merge 1 commit intomasterfrom
kevinschaper wants to merge 1 commit intomasterfrom
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Adds a new `biological attribute` class as a subclass of `attribute` to properly represent OBA (Ontology of Biological Attributes) terms. This addresses the semantic distinction between biological attributes (neutral, measurable characteristics) and phenotypic features (which may denote abnormality). - Added `biological attribute` class with comprehensive description and examples - Added OBA and VT prefixes to support the new class - Includes mappings to OBA:0000001 (root term) and PATO:0000001 (characteristic) - Provides verified examples from OLS: lysine in blood amount, trochanter size, etc. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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@kevinschaper - how does this attribute class differ from clinical finding, clinical attribute? are clinical attributes subclasses of biological attributes? (axis of differentiation in this case would be species maybe, human vs. other vertabrate). |
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Summary
biological attributeclass as a subclass ofattributeto support OBA (Ontology of Biological Attributes) termsMotivation
OBA terms represent biological attributes/traits that are conceptually distinct from phenotypes:
The Biolink model currently conflates these concepts by only having "trait" as an alias of
phenotypic feature(see comment at biolink_model.yaml:8552).Changes
New Class:
biological attributeattribute(notbiological entity)biological sexis already modeled as an attributeNew Prefixes
http://purl.obolibrary.org/obo/OBA_http://purl.obolibrary.org/obo/VT_(Vertebrate Trait Ontology, integrated into OBA)References
🤖 Generated with Claude Code