Review: abnormalPigmentation

[srobb1]

abnormalPigmentation.yaml

If I am understanding the concerns of @sbello here in PR:https://github.com/obophenotype/upheno/pull/339 I think this pattern should be renamed to

• abnormalPigmentationInLocation or
• abnormalPigmenationInAnatomicalEntity or
• abnomalPigmentationInOrgan (if restricted to organ).

The same would apply to

• increasedPigmentation.yaml
• decreasedPigmentaion.yaml
• lossOfPigmentaion.yaml

[sbello]

We're going to want either the first or second option as the entity is often smaller/more specific than an entire organ.

[srobb1]

@sbello Sounds good to me! I just created a PR https://github.com/obophenotype/upheno/pull/351 with the changes.

[matentzn]

I do think we will need the abnormal pigmentation process variants eventually, but for now this looks good. I am slowly beginning to think that I would like patterns to come with a "decreased", "increased" modification option to stop this huge proliferation of patterns; But lets roll with it for now, something like

pigmented and inheres is part of X and has modifier some abnormal and has modifier some decreased

[nicolevasilevsky]

@matentzn yes, it would be so nice if the patterns could include abnormal, increased and decreased and we wouldn't need separate patterns for each of those.

[nicolevasilevsky]

pattern_name: abnormalPigmentationOfAnatomicalEntity pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalPigmentationAnatomicalEntity description: "Any change in the amount of pigmentation in an anatomical Entity. i.e. Abnormal pigmentation of the epidermis"

classes: abnormal: PATO:0000460 anatomical entity: UBERON:0001062 degree of pigmentation: PATO:0002247

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: "abnormal degree of pigmentation of the %s" vars:

• anatomical_entity

annotations:

annotationProperty: exact_synonym
text: "abnormal pigmentation of the %s"
vars:
 - anatomical_entity     

def: text: "abnormal degree of pigmentation of the %s." vars: - anatomical_entity

equivalentTo: text: "'has_part' some ('degree of pigmentation' 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.

[chris-grove]

Can we name this pattern "abnormalPigmentationAmountOfAnatomicalEntity" or something? I would imagine that a pattern called "abnormalPigmentationOfAnatomicalEntity" could apply in cases where the quality of the pigmentation changes (color, hue, pattern, etc.) but the degree/amount isn't necessarily affected. So, can we either change the pattern label, or broaden the meaning, or make separate patterns for general pigmentation abnormalities and degree/amount abnormalities specifically?