---
pattern_name: perforateAnatomicalEntity

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

description: "Use this pattern for phenotypes when an anatomical entity has an
  abnormal hole or a series of holes. Consider the alternative 'PATO:0000609
  closure incomplete' pattern for anatomical entities where a hole is present
  normally at one developmental period but it remains open."

#  examples:
#    - http://purl.obolibrary.org/obo/ZP_0002341  # retina perforate, abnormal
#    - http://purl.obolibrary.org/obo/HP_0100583  # Corneal perforation
#    - http://purl.obolibrary.org/obo/MP_0030414  # tympanic membrane perforation

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

classes:
  perforate: PATO:0002112
  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
  related_synonym: oio:hasRelatedSynonym

vars:
  anatomical_entity: "'anatomical_entity'"

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

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

def:
  text: "The presence of one or more abnormal holes in %s."
  vars:
    - anatomical_entity

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