review: mislocalisedAnatomicalEntity

[chris-grove]

Pattern: https://github.com/obophenotype/upheno/blob/master/src/patterns/dosdp-dev/mislocalisedAnatomicalEntity.yaml

pattern_name: mislocalisedAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/mislocalisedAnatomicalEntity.yaml
description : "Abnormal anatomic location of the an anatomicaly entity, such as HP_0012731 'Ectopic anterior pituitary gland'."

contributors:
  - https://orcid.org/0000-0002-7356-1779
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0001-9076-6015

classes:
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  mislocalised: PATO:0000628

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"

name:
  text: "Abnormally localised %s"
  vars:
   - anatomical_entity

def:
  text: "An abnormally localised %s."
  vars:
    - anatomical_entity

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

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

[chris-grove]

Question has come up: Should abnormal presence of an anatomical entity (not normally present in that organism, e.g. female reproductive organ appearing in males) be considered "ectopic"/"mislocalized" or should there be a separate pattern for "abnormalPresenceOfAnatomicalEntity"?

[sbello]

The MP has the term true hermaphroditism but the EQ uses the PATO term hermaphrodite has part some ( PATO_0001340 and inheres in some UBERON_0000468 and RO_0002573 some PATO_0000460) I don't think we have any other terms for abnormal presence of an anatomical entity that have logical definitions. We do have 'ovotestis' but that does not have a logical definition. I would be very reluctant to use mislocalized or ectopic for this, so I think an "abnormalPresenceOfAnatomicalEntity" pattern could be useful.

[chris-grove]

Would others be OK with making this the pattern for "ectopic" terms? Or do we feel we need a separate pattern? If we're ok with this pattern for "ectopic" terms, does anyone object to adding an exact synonym "ectopic %s"?

[matentzn]

@dosumis can you further the discussion on this :P Thanks!

[nicolevasilevsky]

We discussed this on the phenotype call today:

• we recommend creating a new "abnormalPresenceOfAnatomicalEntity" pattern for @chris-grove's use case
• no objections to adding an exact synonym "ectopic %s"