abnormalFunctionality: inheres in vs. inheres in part

[LCCarmody]

I know this has been explained to death, but I still am not sure which is correct. And searching through HP, it is almost evenly split between the 2. Ex. 'has part' some (functionality and ('inheres in' some hypothalamus) and ('has modifier' some abnormal)) vs. 'has part' some (functionality and ('inheres in part of' some spleen) and ('has modifier' some abnormal))

And the decreasedFunctionalityInLocation and increasedFunctionalityInLocation pattern suggestions don't. Sorry, I hate to be a pain, but I don't know which it should be. Thanks. @srobb1 @matentzn @cmungall @balhoff @nicolevasilevsky

[matentzn]

Good catch. This is the main topic of thursdays Phenotype call. Let’s postpone discussions till then.

[nicolevasilevsky]

pattern_name: abnormalFunctionalityOfAnatomicalEntity pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalFunctionalityOfAnatomicalEntity.yaml description: "Dysfunction of an entity, such as an anatomical entity, like an organ, for example HP_0030964 'Abnormal aortic physiology'"

classes: functionality: PATO:0001509 abnormal: PATO:0000460 anatomical entity: UBERON:0001062

relations: inheres_in: RO:0000052 has_modifier: RO:0002573 has_part: BFO:0000051

annotationProperties: exact_synonym: oio:hasExactSynonym

vars: anatomical_entity: "'anatomical entity'"

name: text: "abnormality of %s physiology" vars:

• anatomical_entity

def: text: "Any functional anomaly of the %s." vars: - anatomical_entity

equivalentTo: text: "'has_part' some ('functionality' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))" vars: - anatomical_entity

@obophenotype/phenotype-editors could you all review this pattern above and sign off on it in the spreadsheet. Nico hopes to have these all reviewed by mid-March, in time for the workshop at Biocuration2019.

[matentzn]

@nicolevasilevsky Would you mind creating the abnormalFunctionalityOfPartOfAnatomicalEntity.yaml pattern as well? just the same as abnormalFunctionalityOfAnatomicalEntity.yaml, just using inheres in part of.

[nicolevasilevsky]

@matentzn I created a PR: https://github.com/obophenotype/upheno/pull/568