pattern_name: disorganizedAnatomicalEntity

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

description: "Use this pattern when an anatomical entity is structurally disorganized, e.g. in case of a disorganized corneal epithelium. Do not use this pattern for fragmented or otherwise broken anatomical entities, even though you might argue that in some sense there is disorganisation in those cases as well. However, those cases belong to different phenotype patterns that are covered by structural phenotype terms in PATO that are different from the 'disorganized' quality."

#  examples:
#    - http://purl.obolibrary.org/obo/MP_0031131  # myocardial fiber disarray
#    - http://purl.obolibrary.org/obo/MP_0020859  # disorganized corneal epithelium
#    - http://purl.obolibrary.org/obo/XPO_0115471  # abnormally disorganized myotome
#    - http://purl.obolibrary.org/obo/ZP_0000138  # chondrocyte disorganized, abnormal

contributors:
  - https://orcid.org/0000-0001-8314-2140  # Ray Stefancsik
  - https://orcid.org/0000-0002-7073-9172  # David Osumi-Sutherland
  - https://orcid.org/0000-0003-4606-0597  # Susan Bello
  - https://orcid.org/0000-0002-9900-7880  # Yvonne M. Bradford

classes:
  disorganized: PATO:0000937
  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: "disorganized %s"
  vars:
    - anatomical_entity

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

def:
  text: "Disorganization of %s."
  vars:
    - anatomical_entity

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