Fixes #2904 - NTR subclasses of nasal tuft cell

[Caroline-99]

Fixes #2904

• Added two terms tuft cell of olfactory epithelium and tuft cell of nasal cavity respiratory epithelium.

• Fixed logical definition of olfactory epithelial cell and basal cell of olfactory epithelium.

[Caroline-99]

#gogoeditdiff

[github-actions]

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/2025-02-10/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/2025-02-10/cl-base.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl

Ontology imports

Ontology annotations

GO_0072091 http://purl.obolibrary.org/obo/GO_0072091

Added

• Class: GO_0072091

basal cell of olfactory epithelium http://purl.obolibrary.org/obo/CL_0002169

Removed

• basal cell of olfactory epithelium EquivalentTo olfactory epithelial cell and (BFO_0000050 some UBERON_0001997)

• basal cell of olfactory epithelium SubClassOf epithelial cell of upper respiratory tract

• basal cell of olfactory epithelium SubClassOf neural cell

• basal cell of olfactory epithelium SubClassOf BFO_0000050 some UBERON_0001997

Added

• basal cell of olfactory epithelium EquivalentTo olfactory epithelial cell and (BFO_0000050 some UBERON_0000482)

• basal cell of olfactory epithelium SubClassOf BFO_0000050 some UBERON_0000482

olfactory epithelial cell http://purl.obolibrary.org/obo/CL_0002167

Removed

• olfactory epithelial cell EquivalentTo epithelial cell and (RO_0002215 some GO_0050911)

Added

• olfactory epithelial cell EquivalentTo epithelial cell and (BFO_0000050 some UBERON_0001997)

• olfactory epithelial cell SubClassOf BFO_0000050 some UBERON_0001997

• olfactory epithelial cell SubClassOf epithelial cell of upper respiratory tract

• olfactory epithelial cell SubClassOf neural cell

olfactory epithelial supporting cell http://purl.obolibrary.org/obo/CL_0000853

Removed

• olfactory epithelial supporting cell SubClassOf basal cell of olfactory epithelium

Added

• olfactory epithelial supporting cell SubClassOf olfactory epithelial cell

tuft cell of nasal cavity respiratory epithelium http://purl.obolibrary.org/obo/CL_4052038

Added

• tuft cell of nasal cavity respiratory epithelium hasRelatedSynonym "tuft-solitary chemosensory cell"

  • hasDbXref "PMID:38306414"

• tuft cell of nasal cavity respiratory epithelium IAO_0000115 "A tuft cell that is part of the nasal cavity respiratory epithelium. Acting as a chemosensor, it detects bitter taste ligands and bacterial signals via taste receptors, maintaining epithelial-microbial homeostasis by stimulating antimicrobial peptide secretion from adjacent epithelial cells. This cell is a major source of IL-25, promoting type 2 immune responses and potentially contributing to chronic rhinosinusitis (O'Leary et al., 2019)."

• tuft cell of nasal cavity respiratory epithelium label "tuft cell of nasal cavity respiratory epithelium"

• tuft cell of nasal cavity respiratory epithelium hasRelatedSynonym "nasal respiratory solitary chemosensory cell"

  • hasDbXref "PMID:38306414"

• tuft cell of nasal cavity respiratory epithelium hasRelatedSynonym "Gɑ-gustducin high respiratory tuft cell"

  • hasDbXref "PMID:38306414"

• tuft cell of nasal cavity respiratory epithelium contributor 0009-0000-8480-9277

• tuft cell of nasal cavity respiratory epithelium date "2025-02-06T15:28:14Z"^^dateTime

• Class: tuft cell of nasal cavity respiratory epithelium

• tuft cell of nasal cavity respiratory epithelium EquivalentTo brush cell and (BFO_0000050 some UBERON_0005385)

• tuft cell of nasal cavity respiratory epithelium SubClassOf tuft cell of nasal cavity

• tuft cell of nasal cavity respiratory epithelium SubClassOf BFO_0000050 some UBERON_0005385

tuft cell of olfactory epithelium http://purl.obolibrary.org/obo/CL_4052037

Added

• tuft cell of olfactory epithelium IAO_0000115 "A tuft cell that is part of the olfactory epithelium, characterized by a globular body and the expression of neurogranin (Nrgn) in mice. This cell plays a crucial role in allergen recognition and regulating olfactory stem cell proliferation via TRPM5-dependent ATP sensing and cysteinyl leukotriene production. Unlike nasal respiratory tuft cells, it has low to absent expression of taste receptors, including the G protein Gα gustducin, and rarely contacts olfactory sensory neurons directly."

  • hasDbXref "doi:/10.1101/2022.09.26.509561"

  • hasDbXref "PMID:38306414"

• tuft cell of olfactory epithelium label "tuft cell of olfactory epithelium"

• tuft cell of olfactory epithelium contributor 0009-0000-8480-9277

• tuft cell of olfactory epithelium hasRelatedSynonym "tuft-microvillous cell"

  • hasDbXref "PMID:38306414"

• tuft cell of olfactory epithelium date "2025-02-06T15:03:53Z"^^dateTime

• tuft cell of olfactory epithelium hasExactSynonym "olfactory tuft cell"

  • hasDbXref "PMID:38306414"

• tuft cell of olfactory epithelium hasRelatedSynonym "TRPM5+ microvillous cell"

  • hasDbXref "PMID:38306414"

• Class: tuft cell of olfactory epithelium

• tuft cell of olfactory epithelium EquivalentTo brush cell and (BFO_0000050 some UBERON_0001997)

• tuft cell of olfactory epithelium SubClassOf RO_0002215 some GO_0072091

• tuft cell of olfactory epithelium SubClassOf olfactory epithelial cell

• tuft cell of olfactory epithelium SubClassOf tuft cell of nasal cavity

[github-actions]

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

basal cell of olfactory epithelium http://purl.obolibrary.org/obo/CL_0002169

Removed

• basal cell of olfactory epithelium EquivalentTo olfactory epithelial cell and (part of some olfactory epithelium)

Added

• basal cell of olfactory epithelium EquivalentTo olfactory epithelial cell and (part of some basal lamina of epithelium)

olfactory epithelial cell http://purl.obolibrary.org/obo/CL_0002167

Removed

• olfactory epithelial cell EquivalentTo epithelial cell and (capable of some detection of chemical stimulus involved in sensory perception of smell)

Added

• olfactory epithelial cell EquivalentTo epithelial cell and (part of some olfactory epithelium)

• olfactory epithelial cell SubClassOf capable of some detection of chemical stimulus involved in sensory perception of smell

tuft cell of nasal cavity respiratory epithelium http://purl.obolibrary.org/obo/CL_4052038

Added

• tuft cell of nasal cavity respiratory epithelium has_related_synonym "tuft-solitary chemosensory cell"

  • database_cross_reference "PMID:38306414"

• tuft cell of nasal cavity respiratory epithelium definition "A tuft cell that is part of the nasal cavity respiratory epithelium. Acting as a chemosensor, it detects bitter taste ligands and bacterial signals via taste receptors, maintaining epithelial-microbial homeostasis by stimulating antimicrobial peptide secretion from adjacent epithelial cells. This cell is a major source of IL-25, promoting type 2 immune responses and potentially contributing to chronic rhinosinusitis (O'Leary et al., 2019)."

• tuft cell of nasal cavity respiratory epithelium label "tuft cell of nasal cavity respiratory epithelium"

• tuft cell of nasal cavity respiratory epithelium has_related_synonym "nasal respiratory solitary chemosensory cell"

  • database_cross_reference "PMID:38306414"

• tuft cell of nasal cavity respiratory epithelium date "2025-02-06T15:28:14Z"^^dateTime

• tuft cell of nasal cavity respiratory epithelium has_related_synonym "Gɑ-gustducin high respiratory tuft cell"

  • database_cross_reference "PMID:38306414"

• tuft cell of nasal cavity respiratory epithelium contributor 0009-0000-8480-9277

• Class: tuft cell of nasal cavity respiratory epithelium

• tuft cell of nasal cavity respiratory epithelium EquivalentTo brush cell and (part of some nasal cavity respiratory epithelium)

tuft cell of olfactory epithelium http://purl.obolibrary.org/obo/CL_4052037

Added

• tuft cell of olfactory epithelium definition "A tuft cell that is part of the olfactory epithelium, characterized by a globular body and the expression of neurogranin (Nrgn) in mice. This cell plays a crucial role in allergen recognition and regulating olfactory stem cell proliferation via TRPM5-dependent ATP sensing and cysteinyl leukotriene production. Unlike nasal respiratory tuft cells, it has low to absent expression of taste receptors, including the G protein Gα gustducin, and rarely contacts olfactory sensory neurons directly."

  • database_cross_reference "doi:/10.1101/2022.09.26.509561"

  • database_cross_reference "PMID:38306414"

• tuft cell of olfactory epithelium has_related_synonym "TRPM5+ microvillous cell"

  • database_cross_reference "PMID:38306414"

• tuft cell of olfactory epithelium label "tuft cell of olfactory epithelium"

• tuft cell of olfactory epithelium contributor 0009-0000-8480-9277

• tuft cell of olfactory epithelium has_related_synonym "tuft-microvillous cell"

  • database_cross_reference "PMID:38306414"

• tuft cell of olfactory epithelium date "2025-02-06T15:03:53Z"^^dateTime

• tuft cell of olfactory epithelium has_exact_synonym "olfactory tuft cell"

  • database_cross_reference "PMID:38306414"

• Class: tuft cell of olfactory epithelium

• tuft cell of olfactory epithelium EquivalentTo brush cell and (part of some olfactory epithelium)

• tuft cell of olfactory epithelium SubClassOf capable of some regulation of stem cell proliferation

[aleixpuigb]

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