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Fixes #2903 tuft cell of nasal cavity #2918

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merged 5 commits into from
Jan 28, 2025
Merged

Fixes #2903 tuft cell of nasal cavity #2918

merged 5 commits into from
Jan 28, 2025

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Caroline-99
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Fixes #2903

Added a new term with textual and logical defs, synonyms and references

@Caroline-99
Fixes #2903 tuft cell of nasal cavity
3cdca0a 
Fixes #2903

Added a new term with textual and logical defs, synonyms and references
@Caroline-99 Caroline-99 linked an issue Jan 21, 2025 that may be closed by this pull request
[NTR] tuft cell of nasal cavity #2903
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@Caroline-99 Caroline-99 self-assigned this Jan 21, 2025
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#gogoeditdiff

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github-actions bot commented Jan 21, 2025 •
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Here's a diff of how these changes impact the classified ontology (on -base file):

Ontology comparison

Left

  • Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-base.owl
  • Version IRI: http://purl.obolibrary.org/obo/cl/releases/2025-01-27/cl-base.owl
  • Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-master.owl/cl-base.owl

Right

  • Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-base.owl
  • Version IRI: http://purl.obolibrary.org/obo/cl/releases/2025-01-27/cl-base.owl
  • Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl

Ontology imports

Ontology annotations

tuft cell of nasal cavity http://purl.obolibrary.org/obo/CL_4052036

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github-actions bot commented Jan 21, 2025 •
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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

tuft cell of nasal cavity http://purl.obolibrary.org/obo/CL_4052036

Added

aleixpuigb
aleixpuigb requested changes Jan 22, 2025
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See inline comments

src/ontology/cl-edit.owl Outdated
EquivalentClasses(obo:CL_4052034 ObjectIntersectionOf(obo:CL_0002204 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0003846)))
SubClassOf(obo:CL_4052034 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002124))
SubClassOf(obo:CL_4052034 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0002491))
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30379593") Annotation(oboInOwl:hasDbXref "PMID:38306414") obo:IAO_0000115 obo:CL_4052036 "A tuft cell that is part of the nasal cavity epithelium, located in both the respiratory and olfactory epithelia of the nose. It shares a core transcriptional profile with other tuft cells, including those in the trachea and intestine, expressing markers such as TRPM5, POU2F3, ChAT, AVIL, and eicosanoid biosynthetic enzymes like ALOX5AP and LTC4S. This cell plays key roles in chemosensation, lipid mediator production, immune responses, and epithelial homeostasis. It is more abundant in the nasal cavity than in the trachea.")
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  • We normally don't add characteristics (in this case markers) that define the parent class. Are there any specific markers?
  • The textual definition states that these cells are found in the trachea, therefore the formal definition is wrong. I understand that there are more tuft cells in the nasal cavity than in the trachea, but tuft cells of nasal cavity, which are restricted to nasal cavity. I would remove this sentence.

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#gogoeditdiff

@Caroline-99 Caroline-99 merged commit 850c710 into master Jan 28, 2025
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@Caroline-99 Caroline-99 deleted the 2903-ntr-tuft-cell-of-nasal-cavity branch January 28, 2025 13:58
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[NTR] tuft cell of nasal cavity
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