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obophenotype / upheno

The Unified Phenotype Ontology (uPheno) integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.
https://obophenotype.github.io/upheno/
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Request new pattern for Incomplete structure #931

Open LCCarmody opened 4 months ago

LCCarmody commented 4 months ago

ZP, XPO use a 'incomplete structure' and now MP and HP will start using this. Need to add a pattern for this.

'has part' some ('Incomplete structure' and ('characteristic of' some Anatomical entity) and ('has modifier' some abnormal))

Refers to https://github.com/obophenotype/human-phenotype-ontology/issues/7389 @anna-anagnostop

sbello commented 4 months ago

Are you sure we want characteristic of and not characteristic of part of? I think we would want characteristic of part of, if part of the entity is incomplete then the entity as a whole is incomplete.

example incomplete mitral valve leaflet would be a child of incomplete mitral valve

LCCarmody commented 4 months ago

Remind me how far that goes up? If it is an incomplete cochlea, what would 'characteristic of part of' mean? An incomplete 'inner ear', yes. An 'incomplete ear', I don't know.

sbello commented 4 months ago

Yeah, I think it would go all the way up the part tree. We had a request to see what exactly happens (see https://github.com/obophenotype/upheno/issues/925) The spreadsheets are ready to go for this we just need to push the next steps through. From my perspective if part of the ear is incomplete the ear is incomplete but I don't know that a clinician would agree.

pnrobinson commented 4 months ago

An incomplete structure of the inner ear would be regarded as an incomplete structure of the ear by the clinician, but probably no clinician would say incomplete ear for this.