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Add abnormally dilated cellular component template #892

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59 changes: 59 additions & 0 deletions src/patterns/dosdp-dev/abnormallyDilatedCellularComponent.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,59 @@
---
pattern_name: abnormallyDilatedCellularComponent

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

description: 'Use this phenotype pattern when a cellular component is wider,
larger or further open than usual in all dimensions. In contrast to a
"PATO:0001851 swollen" entity, the size increase is not transient.'

# examples:
# - http://purl.obolibrary.org/obo/MP_0004089 # dilated sarcoplasmic reticulum
# - http://purl.obolibrary.org/obo/MP_0011632 # dilated mitochondrion
# - http://purl.obolibrary.org/obo/HP_0030774 # Mitochondrial swelling
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Is this a transient swelling phenotype or non-transient dilation?
Need conformation from HPO that this example is correct.

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@ybradford ybradford Oct 20, 2022

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here is a ZP example ZP:0012665 http://purl.obolibrary.org/obo/ZP_0012665 Golgi apparatus cholangiocyte dilated, abnormal

http://purl.obolibrary.org/obo/ZP_0101477 endoplasmic reticulum liver dilated, abnormal

ORCiD: 0000-0002-9900-7880


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

classes:
dilated: PATO:0001571
abnormal: PATO:0000460
cellular_component: GO:0005575

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

annotationProperties:
exact_synonym: oio:hasExactSynonym
related_synonym: oio:hasRelatedSynonym

vars:
cellular_component: "'cellular_component'"

name:
text: "dilated %s"
vars:
- cellular_component

annotations:
- annotationProperty: related_synonym
text: "swollen %s"
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@rays22 rays22 Oct 20, 2022

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Remove this synonym, because it is misleading.

vars:
- cellular_component

def:
text: "A dilated %s that is wider or larger in all dimensions."
vars:
- cellular_component

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