search

obophenotype / upheno

The Unified Phenotype Ontology (uPheno) integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.
https://obophenotype.github.io/upheno/
Creative Commons Zero v1.0 Universal
76 stars 17 forks source link

Review: protrudingMorphologyInLocation #350

Open srobb1 opened 5 years ago

srobb1 commented 5 years ago

protrudingMorphologyInLocation.yaml

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

nicolevasilevsky commented 5 years ago

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:

annotations:

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

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

@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 commented 5 years ago

are these parentheses correct in the equiv axiom?

chris-grove commented 5 years ago

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:

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 commented 5 years ago

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?