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Add exserted anatomical entity pattern template #835

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73 changes: 73 additions & 0 deletions src/patterns/dosdp-dev/exsertedAnatomicalEntity.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,73 @@
---
pattern_name: exsertedAnatomicalEntity

pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/exsertedAnatomicalEntity.yaml

description: 'Use this phenotype pattern when an anatomical entity is
abnormally protruding or projecting from the body. These anatomical
entities may be described as being prolapsed, protuberant or sticking out.'

# examples:
# - http://purl.obolibrary.org/obo/ZP_0016742 # pectoral fin exserted, abnormal
# - http://purl.obolibrary.org/obo/HP_0002035 # Rectal prolapse
# - http://purl.obolibrary.org/obo/MP_0000493 # rectal prolapse
# # - http://purl.obolibrary.org/obo/MP_0009079 # prolapsed intervertebral disk

contributors:
- https://orcid.org/0000-0001-8314-2140 # Ray Stefancsik
- https://orcid.org/0000-0002-7356-1779 # Nicolas Matentzoglu
- https://orcid.org/0000-0003-4606-0597 # Susan Bello
- https://orcid.org/0000-0002-6490-7723 # Anna V. Anagnostopoulos

classes:
exserted: PATO:0000623
abnormal: PATO:0000460
anatomical_entity: UBERON:0001062

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

annotationProperties:
exact_synonym: oio:hasExactSynonym
narrow_synonym: oio:hasNarrowSynonym

vars:
anatomical_entity: "'anatomical_entity'"

name:
text: "exserted %s"
vars:
- anatomical_entity

annotations:
- annotationProperty: exact_synonym
text: "protuberant %s"
vars:
- anatomical_entity

- annotationProperty: narrow_synonym
text: "%s prolapse"
vars:
- anatomical_entity

- annotationProperty: narrow_synonym
text: "prolapsed %s"
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vars:
- anatomical_entity

def:
text: "An exserted %s is protruding or projecting from the body abnormally."
vars:
- anatomical_entity

equivalentTo:
text: "'has_part' some (
'exserted' and
('characteristic_of' some %s) and
('has_modifier' some 'abnormal')
)"
vars:
- anatomical_entity
...