Review: abnormalTopology

[srobb1]

abnormalTopology.yaml

This is a great pattern! I can definitely use this one!! I didn't realized the point was abnormal position with the name abnormalTopology. I probably should have :confused:

Definitely a human readable description is needed, but maybe a new name for those a bit slow like me.

Sofia

[nicolevasilevsky]

I agree a new name would be more intuitive.

[nicolevasilevsky]

pattern_name: abnormalPositionOfAnatomicalEntity pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalPositionOfAnatomicalEntity.yaml description: ""

classes: position: PATO:0000140 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: entity: "'anatomical entity'"

name: text: "abnormal location of %s" vars:

• entity

def: text: "An abnormal location of %s." vars: - entity

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

[sbello]

The MP terms that I created recently have the definition format 'any anomaly in the position of X in relation to other structures' Some of the ones Cindy entered use 'location or orientation'. Based on this I wonder if having just 'location' in the definition is too narrow since want to also cover abnormal orientation. The topoplogy part of the term names was a request from the IMPC folks

[chris-grove]

Can someone explain the difference between "abnormal position"/"abnormal location" and "mislocalized"? We now have the following patterns:

abnormalPositionOfAnatomicalEntity abnormalPositionOfAnatomicalEntityInLocation mislocalisedAnatomicalEntity

[matentzn]

@sbello @nicolevasilevsky can you answer @chris-grove question from HP/MP perspective?

[nicolevasilevsky]

Some examples from HPO are: abnormal position: HP_0010814 'Abnormal position of hair whorl' HP_0000357 'Abnormal location of ears' HP_0100542 'Abnormal localization of kidney'

mislocalised: HP_0001083 'Ectopia lentis' HP_0011742 'Ectopic adrenal gland' HP_0002282 'Gray matter heterotopia'

To be honest, I don't know when one would use abnormal position vs mislocalised in these cases, but it seems like mislocalised is used for ectopia terms (but it seems like 'Abnormal localization of kidney' could maybe be synonymous with ectopic kidney?)

[drseb]

I would guess that @pnrobinson and @cmungall are the best to comment here. I also don't see a clear difference between those pato classes.