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Add dislocated anatomical entity pattern template #829

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58 changes: 58 additions & 0 deletions src/patterns/dosdp-dev/dislocatedAnatomicalEntity.yaml
Original file line number Diff line number Diff line change
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---
pattern_name: dislocatedAnatomicalEntity

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

description: 'Use this pattern for phenotypes, e.g. elbow dislocation, where the spatial location of the anatomical entity relative to other entities in its vicinity is abnormal or out of its proper place. The anatomical entity is assumed to have had developed in its normal location and something happened to move it out of that position. For ectopic anatomical entities, where the anatomical entity has developed in the wrong location, consider using the "mislocalised PATO:0000628" positional quality pattern.'

# examples:
# - http://purl.obolibrary.org/obo/HP_0001373 # Joint dislocation
# - http://purl.obolibrary.org/obo/HP_0002827 # Hip dislocation
# - http://purl.obolibrary.org/obo/MP_0030795 # joint dislocation
# - http://purl.obolibrary.org/obo/MP_0030796 # hip dislocation
# - http://purl.obolibrary.org/obo/MP_0030843 # elbow dislocation

contributors:
- https://orcid.org/0000-0001-8314-2140 # Ray Stefancsik
- https://orcid.org/0000-0003-4606-0597 # Susan Bello

classes:
dislocated: PATO:0001852
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

vars:
anatomical_entity: "'anatomical_entity'"

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

annotations:
- annotationProperty: exact_synonym
text: "dislocation of %s"
vars:
- anatomical_entity

def:
text: "Dislocation or displacement of %s. The effected anatomical entity is assumed to have had developed in its normal location before the dislocation."
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OK

vars:
- anatomical_entity

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