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obophenotype / upheno

The Unified Phenotype Ontology (uPheno) integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.
https://obophenotype.github.io/upheno/
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Review: abnormalNumberOfAnatomyByType #348

Open srobb1 opened 5 years ago

srobb1 commented 5 years ago

abnormalNumberOfAnatomyByType.yaml

Name should probably be abnormalNumberOfAnatomyByQuantityType

nicolevasilevsky commented 5 years ago

I think this could generate some strange labels, like 'altered number of platelets' or 'has extra parts of type adipose tissue.'

It would probably be better to separate these into a pattern for each PATO quality, then you could write the definition differently. For example:

pattern_name: abnormalNumberOfAnatomy pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns/abnormalNumberOfAnatomy.yaml

classes: altered_number_of: PATO:0002083 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: anatomical_entity: "'entity'" altered_number_of: "'quantity'"

name: text: "Abnormal number of %s" vars:

annotations: annotationProperty: exact_synonym text: "Abnormal %s count" vars:

def: text: "Any anomaly that causes there to be an abnormal number of %s." vars:

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

srobb1 commented 5 years ago

@nicolevasilevsky That is probably the right thing to do. I will change this one and add more patterns.

nicolevasilevsky commented 5 years ago

@srobb1- talking to @matentzn right now - we are going to fix PATO, so the pattern that you created will work, ignore my comments above