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Fixes #2578 -NTR- fibroblastic reticular cell #2581

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merged 3 commits into from
Sep 23, 2024
Merged

Fixes #2578 -NTR- fibroblastic reticular cell #2581

merged 3 commits into from
Sep 23, 2024

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Caroline-99
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  • Added a new term
  • Added textual and logical definition with extended description
  • Added synonyms
  • Added references

@Caroline-99
Fixes #2578
f5778d7 
- Added a new term
- Added textual and logical definition with extended description
- Added synonyms
- Added references
@Caroline-99 Caroline-99 linked an issue Sep 19, 2024 that may be closed by this pull request
[NTR] intestinal fibroblastic reticular cell #2578
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@Caroline-99 Caroline-99 self-assigned this Sep 19, 2024
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#gogoeditdiff

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Here's a diff of how these changes impact the classified ontology (on -simple file):

Ontology comparison

Left

  • Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-simple.owl
  • Version IRI: http://purl.obolibrary.org/obo/cl/releases/2024-09-19/cl-simple.owl
  • Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-master.owl/cl-simple.owl

Right

  • Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-simple.owl
  • Version IRI: http://purl.obolibrary.org/obo/cl/releases/2024-09-19/cl-simple.owl
  • Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl

Ontology imports

Ontology annotations

intestinal fibroblastic reticular cell http://purl.obolibrary.org/obo/CL_4052004

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Here's a diff of your edit file (unreasoned)

Ontology comparison

Left

  • Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
  • Version IRI: None
  • Loaded from: file:/__w/cell-ontology/cell-ontology/master/src/ontology/cl-edit.owl

Right

  • Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
  • Version IRI: None
  • Loaded from: file:/__w/cell-ontology/cell-ontology/branch/src/ontology/cl-edit.owl

Ontology imports

Ontology annotations

intestinal fibroblastic reticular cell http://purl.obolibrary.org/obo/CL_4052004

Added

aleixpuigb
aleixpuigb requested changes Sep 20, 2024
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Please, see inline comments.

src/ontology/cl-edit.owl Outdated
@@ -32470,6 +32471,20 @@ AnnotationAssertion(rdfs:label obo:CL_4052003 "intestinal villus capillary endot
EquivalentClasses(obo:CL_4052003 ObjectIntersectionOf(obo:CL_0002144 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001213)))
SubClassOf(obo:CL_4052003 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0002064))

# Class: obo:CL_4052004 (intestinal fibroblastic reticular cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33707780") Annotation(oboInOwl:hasDbXref "doi:/10.1038/s41467-022-29734-2") obo:IAO_0000115 obo:CL_4052004 "A specialized fibroblastic reticular cell that is part of gut-associated lymphoid tissues(GALT), responsible for forming a structural network that facilitates immune cell interactions. This cell is found in Peyer's patches, cryptopatches, and isolated lymphoid follicles. It plays crucial roles in maintaining intestinal immunity by controlling innate lymphoid cell homeostasis and function, organizing lymphoid structures, and contributing to intestinal microbiome balance.")
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Please remove other terms abbreviations (GALT) (it is also lacking an space). Also, I would use the singular form for the tissue.

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I agree that abbreviations should not be used on there own, but I don't see a problem with including the abbreviation in brackets after the full terms. The vast majority of the literature uses GALT, so I think important for users to see this.

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@aleixpuigb aleixpuigb Sep 20, 2024 •
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I don't think we currently have a guideline about including other term abbreviations in the definition, and if we want to add them we should include this in the document. Personally, I think that other terms abbreviations and definitions should be restricted to those terms, but overall I want cohesion on the style so if it is more helpful to include them I don't have a problem as long as it is in the guidelines.

@Caroline-99 Caroline-99 added this to the pre HCA meeting release milestone Sep 23, 2024
@Caroline-99 Caroline-99 merged commit 9498f36 into master Sep 23, 2024
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@Caroline-99 Caroline-99 deleted the 2578-ntr-intestinal-fibroblastic-reticular-cell branch September 23, 2024 14:13
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@aleixpuigb aleixpuigb aleixpuigb approved these changes

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[NTR] intestinal fibroblastic reticular cell
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