Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add 'abnormally scaly anatomical entity' pattern template #896

Draft
wants to merge 1 commit into
base: master
Choose a base branch
from
Draft
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
61 changes: 61 additions & 0 deletions src/patterns/dosdp-dev/abnormallyScalyAnatomicalEntity.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,61 @@
---
pattern_name: abnormallyScalyAnatomicalEntity

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

description: 'Use this phenotype pattern when the surface of an anatomical
entity is abnormally covered with scales, or when it is scaling. It is
scaling when the surface or the anatomical entity has small, hard, dry areas
that fall off in small pieces.'

# examples:
# - http://purl.obolibrary.org/obo/MP_0000020 # scaly ears
# - http://purl.obolibrary.org/obo/ZP_0002670 # endothelial cell atrioventricular canal endocardium scaly, abnormal
# - http://purl.obolibrary.org/obo/MP_0001192 # scaly skin
# - http://purl.obolibrary.org/obo/HP_0040189 # Scaling skin

contributors:
- https://orcid.org/0000-0001-8314-2140 # Ray Stefancsik

classes:
scaly: PATO:0001804
Copy link
Contributor Author

@rays22 rays22 Dec 1, 2022

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

PATO definition looks problematic.

  • Create a PATO ticket to address this. Need to distinguish it from normal fish/bird scales: skin surface qualities vs. skin appendages.

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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: "scaly %s"
vars:
- anatomical_entity

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

def:
text: "An abnormal surface of %s which is covered with scales or it has
small, hard, dry areas that fall off in small pieces."
vars:
- anatomical_entity

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