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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: abnormalBehavior.yaml #331

Closed ybradford closed 5 years ago

ybradford commented 5 years ago

abnormalBehavior.yaml

For classes Behavior process is NBO behavior process. Does this mean that GO behavior processes are excluded? ZFIN uses GO for behavior currently (swimming behavior GO:0036269, locomotory behavior GO:0007626 for example). Maybe ZFIN will need to consider moving to NBO, but restricting to NBO right now will mean ZP behaviors will be done as processes. Maybe that is ok, but these should be considered for reconciliation.

nicolevasilevsky commented 5 years ago

This wasn't intentional, @ybradford, we should revise the pattern to include GO behaviors.

matentzn commented 5 years ago

this will be captured by OBO core hopefully. Both GO and NBO behaviour must be usable for behavior patterns!

sbello commented 5 years ago

Looking at the MP patterns we have terms that use NBO, terms that use GO (MP:0001422 for example), and a few terms that use UBERON (MP:0004262, MP:0009434). The ones I've found using UBERON relate to strength or paralysis. So I think we're going to need to review and potentially broaden the parent pattern.

matentzn commented 5 years ago 
pattern_name: abnormalBehavior
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalBehavior.yaml
description: "Any unspecified abnormality of a behavior."

classes:
  process quality: PATO:0001236
  abnormal: PATO:0000460
  behavior process: NBO:0000313

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym 

vars:
  behavior_process: "'behavior process'"

name:
  text: "abnormal %s"
  vars:
   - behavior_process

def:
  text: "An anomaly in %s."
  vars:
    - behavior_process

equivalentTo:
  text: "'has_part' some ('process quality' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - behavior_process

@obophenotype/phenotype-editors please sign off

matentzn commented 5 years ago

(filler will be OBOCORE:behavior once it is available)

chris-grove commented 5 years ago

I agree about the whole NBO vs GO issue. It would be good to know if one subsumes the other, but it sounds like the intention is to use OBOCORE:behavior which should encompass everything, in which case I'm OK with it.

Looks good.

matentzn commented 5 years ago

Consolidated for now; lets review when this comes up again.