Review: protrudingMorphologyInLocation

[srobb1]

protrudingMorphologyInLocation.yaml

There are more spaces than normal in the equivalentTo variable list.

[nicolevasilevsky]

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

classes: abnormal: PATO:0000460 anatomical entity: UBERON:0001062 protruding out of: PATO:0001646

relations: inheres_in: RO:0000052 has_modifier: RO:0002573 has_part: BFO:0000051 part_of: BFO:0000050 towards: RO:0002503

annotationProperties: exact_synonym: oio:hasExactSynonym

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

name: text: "abnormal protrusion of % through %" vars:

• anatomical_entity
• location

annotations:

• annotationProperty: exact_synonym text: "" vars:
  • anatomical_entity
  • location

def: text: "hernial protrusion of the % through an opening or defect in the %." vars: - anatomical_entity - location

equivalentTo: text: "'has_part' some ('protruding out of' and ('inheres_in' some (%s) and ('towards' 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.

[nicolevasilevsky]

are these parentheses correct in the equiv axiom?

[chris-grove]

WRT parentheses I think there are 5 opening parentheses and 4 closing; I think the 'inheres_in' phrase doesn't need opening and closing parentheses around %s, so should just be:

equivalentTo: text: "'has_part' some ('protruding out of' and ('inheres_in' some %s) and ('towards' some %s) and ('has_modifier' some abnormal))" vars:

• anatomical_entity
• location

but that's how it is in the current file:

https://github.com/obophenotype/upheno/blob/master/src/patterns/dosdp-dev/abnormallyProtrudingAnatomicalEntityInLocation.yaml

so it's fine.

[chris-grove]

Does the textual definition need to include "hernial protrusion" instead of just "protrusion"? Existing definitions of "hernia" I can find refer to the protrusion through an "abnormal opening"; what if it isn't an abnormal opening? Like "protruding teeth"? They are protruding through their normal opening but doing so abnormally? In worms we have the term "cloacal structures protrude", in which structures protrude through their normal opening but do so abnormally. Maybe we can have a pattern that doesn't specify "InLocation" when it is the normal opening?