DRAFT working on #1002 by sbello · Pull Request #1003 · obophenotype/upheno

sbello · 2025-10-01T19:58:44Z

Creating a new pattern for dilated lumen
Needs to be discussed at the editors' call on 10/3/2025

Creating a new pattern for dilated lumen

sabrinatoro

I have a few questions to discuss

do we need the distinction between dilated anatomical lumen and dilated anatomical entity?
if we have a pattern for "dilated anatomical lumen", then it would make more sense to use the anatomical space instead of anatomical entity. (UNLESS this pattern is to refer to the cases where there is no term for the "lumen"... In this case, I have the question above)

sabrinatoro · 2025-10-01T22:00:02Z

+
+pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDilatedAnatomicalEntityLumen.yaml
+
+description: 'An abnormally dilated lumen/cavity/space of anatomical entity, for example, an abnormally dilated capillary lumen. This covers anatomical entities for which there is not separate term for the lumen/cavity/space within the entity. If there is a term for the space within an entity you should us the abnormallyDilatedAnatomicalEntity pattern.'


I like the distinction between lumen/cavity and anatomical entity being separated, because "dilated" most often refers to lumen/cavity. So the questions are

do we need an "abnormallyDilatedAnatomicalEntity pattern"?

do we need the distinction between the dilated anatomical entity and the dilated anatomical cavity?

The existing dilated anatomical entity patter would be reserved for cases where Uberon has a term for the space such as cavity of right atrium (http://purl.obolibrary.org/obo/UBERON_0016522).
This pattern is for the many cases where Uberon has a term for the anatomical entity but NO term for the space/cavity so we need to specify that we are talking about the space.

change the variable to material anatomical entity not the higher level anatomical entity

Typos
This covers anatomical entities for which there is not a separate term for the lumen/cavity/space within the entity. If there is a term for the space within an entity you should use the abnormallyDilatedAnatomicalEntity pattern

sabrinatoro · 2025-10-01T22:04:56Z

+  - annotationProperty: exact_synonym
+    text: "abnormal %s dilation"
+    vars:
+      - anatomical_entity


Since this pattern is to refer to dilated lumen/cavity/space of anatomical entity, I think UBERON:0000464-anatomical space would be more appropriate.

But you want the label to read 'abnormal intestinal dilation' for example and if you are using this pattern there is no term in Uberon specifically for the space

sabrinatoro · 2025-10-01T22:05:12Z

+  - annotationProperty: exact_synonym
+    text: "dilated %s"
+    vars:
+      - anatomical_entity


I think anatomical space would be more appropriate.

pnrobinson · 2025-10-02T02:47:03Z

dilation refers to lumina/cavities. We would not say dilation if a solid anatomical entity was enlarged.

sbello · 2025-10-02T16:22:35Z

@pnrobinson Agreed, this pattern is to make that distinction explicit in the logical definition.

sbello · 2025-10-03T15:18:15Z

Need to update abnormaldilatedanatomicalentity to be use immaterial entity as the variable
https://raw.githubusercontent.com/obophenotype/upheno/master/src/patterns/dosdp-dev/abnormallyDilatedAnatomicalEntity.yaml

anna-anagnostop

Once the proposed changes are put in place, I am fine with this.

abnormallyDilatedAnatomicalEntityLumen Fixed typos in description changed variable to material anatomical entity abnormallyDilatedAnatomicalEntity Added text to description to indicate when each pattern should be used changed title to include Immaterial chanced variable to immaterial anatomical entity

fixed placement of immaterial and changed name of abnormalyDilatedAnatomicalEntity to abnormalyDilatedImmaterialAnatomicalEntity

flipped the name of the existing pattern back to just abnormallyDilatedAnatomicalEntity to avoid breaking downstream dependencies

sabrinatoro

There are a few typos, otherwise it looks great.
Thank you, Sue!

sabrinatoro · 2025-10-06T19:44:39Z

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

-description: 'An abnormally dilated anatomical entity, for example, an abnormally dilated cardiac ventricle.'
+description: 'An abnormally dilated immaterial anatomical entity, for example, an abnormally dilated cavity of a cardiac ventricle. This pattern should be used when there is a term for the lumen/cavity/space within the anatomical entity. If not space term exists use the abnormallyDilatedAnatomicalEntityLumne pattern.'


Typo at the end of abnormallyDilatedAnatomicalEntityLumen

If no space term exists, use the abnormallyDilatedAnatomicalEntityLumen pattern.

sabrinatoro · 2025-10-06T19:53:04Z

+
+pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDilatedAnatomicalEntityLumen.yaml
+
+description: 'An abnormally dilated lumen/cavity/space of anatomical entity, for example, an abnormally dilated capillary lumen. This covers anatomical entities for which there is not a separate term for the lumen/cavity/space within the entity. If there is a term for the space within an entity you should use the abnormallyDilatedAnatomicalEntity pattern.'


The pattern name should be updated to : abnormallyDilatedImmaterialAnatomicalEntity

Suggested change

description: 'An abnormally dilated lumen/cavity/space of anatomical entity, for example, an abnormally dilated capillary lumen. This covers anatomical entities for which there is not a separate term for the lumen/cavity/space within the entity. If there is a term for the space within an entity you should use the abnormallyDilatedAnatomicalEntity pattern.'

description: 'An abnormally dilated lumen/cavity/space of anatomical entity, for example, an abnormally dilated capillary lumen. This covers anatomical entities for which there is not a separate term for the lumen/cavity/space within the entity. If there is a term for the space within an entity you should use the abnormallyDilatedImmaterialAnatomicalEntity.'

Nico asked me not to do that as it would break the downstream uPheno processes.

sabrinatoro · 2025-10-06T19:55:05Z

+  exact_synonym: oio:hasExactSynonym
+
+vars:
+  material_anatomical_entity: "'material anatomical_entity'"


typo: underscore missing between "material" and "anatomical"

Suggested change

material_anatomical_entity: "'material anatomical_entity'"

material_anatomical_entity: "'material_anatomical_entity'"

sabrinatoro · 2025-10-06T19:58:46Z

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

-description: 'An abnormally dilated anatomical entity, for example, an abnormally dilated cardiac ventricle.'
+description: 'An abnormally dilated immaterial anatomical entity, for example, an abnormally dilated cavity of a cardiac ventricle. This pattern should be used when there is a term for the lumen/cavity/space within the anatomical entity. If not space term exists use the abnormallyDilatedAnatomicalEntityLumne pattern.'


Suggested change

description: 'An abnormally dilated immaterial anatomical entity, for example, an abnormally dilated cavity of a cardiac ventricle. This pattern should be used when there is a term for the lumen/cavity/space within the anatomical entity. If not space term exists use the abnormallyDilatedAnatomicalEntityLumne pattern.'

description: 'An abnormally dilated immaterial anatomical entity, for example, an abnormally dilated cavity of a cardiac ventricle. This pattern should be used when there is a term for the lumen/cavity/space within the anatomical entity. If not space term exists use the abnormallyDilatedAnatomicalEntityLumen pattern.'

sabrinatoro · 2025-10-06T19:59:04Z


 vars:
-  anatomical_entity: "'anatomical_entity'"
+  immaterial_anatomical_entity: "'immaterial anatomical_entity'"


Suggested change

immaterial_anatomical_entity: "'immaterial anatomical_entity'"

immaterial_anatomical_entity: "'immaterial_anatomical_entity'"

fixing typos

working on #1002

9a2b0a0

Creating a new pattern for dilated lumen

sbello requested review from anna-anagnostop and sabrinatoro October 1, 2025 19:58

sabrinatoro reviewed Oct 1, 2025

View reviewed changes

anna-anagnostop requested changes Oct 3, 2025

View reviewed changes

sbello added 3 commits October 3, 2025 12:02

working on #1002

b12ed46

fixed placement of immaterial and changed name of abnormalyDilatedAnatomicalEntity to abnormalyDilatedImmaterialAnatomicalEntity

working on #1002

997f07c

flipped the name of the existing pattern back to just abnormallyDilatedAnatomicalEntity to avoid breaking downstream dependencies

sabrinatoro approved these changes Oct 6, 2025

View reviewed changes

working on #1002

c89b80a

fixing typos


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

		description: 'An abnormally dilated lumen/cavity/space of anatomical entity, for example, an abnormally dilated capillary lumen. This covers anatomical entities for which there is not separate term for the lumen/cavity/space within the entity. If there is a term for the space within an entity you should us the abnormallyDilatedAnatomicalEntity pattern.'

	material_anatomical_entity: "'material anatomical_entity'"
	material_anatomical_entity: "'material_anatomical_entity'"

	description: 'An abnormally dilated immaterial anatomical entity, for example, an abnormally dilated cavity of a cardiac ventricle. This pattern should be used when there is a term for the lumen/cavity/space within the anatomical entity. If not space term exists use the abnormallyDilatedAnatomicalEntityLumne pattern.'
	description: 'An abnormally dilated immaterial anatomical entity, for example, an abnormally dilated cavity of a cardiac ventricle. This pattern should be used when there is a term for the lumen/cavity/space within the anatomical entity. If not space term exists use the abnormallyDilatedAnatomicalEntityLumen pattern.'

	immaterial_anatomical_entity: "'immaterial anatomical_entity'"
	immaterial_anatomical_entity: "'immaterial_anatomical_entity'"

Conversation

sbello commented Oct 1, 2025

Uh oh!

sabrinatoro left a comment

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

pnrobinson commented Oct 2, 2025

Uh oh!

sbello commented Oct 2, 2025

Uh oh!

sbello commented Oct 3, 2025

Uh oh!

anna-anagnostop left a comment

Choose a reason for hiding this comment

Uh oh!

sabrinatoro left a comment

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants