Review: abnormalMorphologyInLocation

[srobb1]

abnormalMorphologyInLocation.yaml

I am confused about the 'position' class declaration:

classes:
  position: PATO:0000140

I don't see this mentioned anywhere else in the pattern.

Sofia

[matentzn]

Good catch! Will fix this.

[matentzn]

Please leave this ticket open until the review of the above pattern is completed by 5 or more editors.

[ybradford]

this should probably also be limited to anatomical structures (entity is BFO:0000001)

[nicolevasilevsky]

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

classes: abnormal: PATO:0000460 anatomical entity: UBERON:0001062 morphology: PATO:0000051

relations: inheres_in: RO:0000052 has_modifier: RO:0002573 has_part: BFO:0000051 part_of: BFO:0000050

annotationProperties: exact_synonym: oio:hasExactSynonym

vars: anatomical_entity: "'anatomical entity'" location: "'anatomical entity'"

name: text: "morphological abnormality of the %s in the %s" vars:

• anatomical_entity
• location

annotations:

• annotationProperty: exact_synonym text: "Abnormal %s in the %s" vars:
  • anatomical_entity
  • location

def: text: "A morphological abnormality of the %s in the %s." vars:

• anatomical_entity
• location

equivalentTo: text: "'has_part' some (morphology and ('inheres_in' some (%s and ('part_of' some %s))) and ('has_modifier' some abnormal))" vars:

• anatomical_entity
• location

@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 change the exact synonym to "Abnormal morphology of %s in the %s"? I don't think "Abnormal %s in the %s" is sufficiently specific

[matentzn]

Comments consolidated in http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalMorphologyOfAnatomicalEntityInLocation.yaml closing for now