Fixes #2909 NTR- tuft cell of thymus

[Caroline-99]

Fixes #2909

• Added a new term with textual and logical defs, synonyms and references
• NOTE - GO term cytospinule will be linked to this term once available on GO

[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/2025-01-17/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/2025-01-17/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_0002491 http://purl.obolibrary.org/obo/GO_0002491

Added

• Class: GO_0002491

kidney afferent arteriole endothelial cell http://purl.obolibrary.org/obo/CL_1001096

Removed

• kidney afferent arteriole endothelial cell SubClassOf endothelial cell of artery

tuft cell of thymus http://purl.obolibrary.org/obo/CL_4052034

Added

• tuft cell of thymus hasExactSynonym "thymic tuft cell"

  • hasDbXref "PMID:30904566"

• tuft cell of thymus contributor 0009-0000-8480-9277

• tuft cell of thymus date "2025-01-16T11:29:54Z"^^dateTime

• tuft cell of thymus IAO_0000115 "A tuft cell that is part of the medullary epithelium of the thymus, characterized by lateral microvilli and specific markers, including L1CAM in both mice (Zhang et al., 2022) and humans (Sun et al., 2023), as well as MHC II in mice (Kotas et al., 2023). This cell is pivotal in immune functions such as antigen presentation, central tolerance, and type 2 immunity. A tuft cell in the thymus exhibits characteristics of both a medullary thymic epithelial cell (mTEC) and a peripheral tuft cell. Its development is governed by transcription factors such as POU2F3."

  • hasDbXref "PMID:36961668"

  • hasDbXref "PMID:35668088"

  • hasDbXref "PMID:30904566"

  • hasDbXref "PMID:36351364"

• tuft cell of thymus label "tuft cell of thymus"

• tuft cell of thymus comment "A thymic tuft cell is a subset of terminally differentiated medullary thymic epithelial cell comprising 5-10% of total mTECs. Lineage-tracing studies indicate that this cell arises from mature MHCII mTECs, with development occurring through both Aire-dependent and Aire-independent pathways. However, its exact origins remain unclear."

  • hasDbXref "PMID:30904566"

• Class: tuft cell of thymus

• tuft cell of thymus EquivalentTo brush cell and (BFO_0000050 some UBERON_0003846)

• tuft cell of thymus SubClassOf BFO_0000050 some UBERON_0003846

• tuft cell of thymus SubClassOf RO_0002215 some GO_0002491

• tuft cell of thymus SubClassOf brush cell

• tuft cell of thymus SubClassOf medullary thymic epithelial cell

[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

antigen processing and presentation of endogenous peptide antigen via MHC class II http://purl.obolibrary.org/obo/GO_0002491

Added

• Class: antigen processing and presentation of endogenous peptide antigen via MHC class II

tuft cell of thymus http://purl.obolibrary.org/obo/CL_4052034

Added

• tuft cell of thymus definition "A tuft cell that is part of the medullary epithelium of the thymus, characterized by lateral microvilli and specific markers, including L1CAM in both mice (Zhang et al., 2022) and humans (Sun et al., 2023), as well as MHC II in mice (Kotas et al., 2023). This cell is pivotal in immune functions such as antigen presentation, central tolerance, and type 2 immunity. A tuft cell in the thymus exhibits characteristics of both a medullary thymic epithelial cell (mTEC) and a peripheral tuft cell. Its development is governed by transcription factors such as POU2F3."

  • database_cross_reference "PMID:35668088"

  • database_cross_reference "PMID:36961668"

  • database_cross_reference "PMID:30904566"

  • database_cross_reference "PMID:36351364"

• tuft cell of thymus has exact synonym "thymic tuft cell"

  • database_cross_reference "PMID:30904566"

• tuft cell of thymus label "tuft cell of thymus"

• tuft cell of thymus contributor 0009-0000-8480-9277

• tuft cell of thymus date "2025-01-16T11:29:54Z"^^dateTime

• tuft cell of thymus comment "A thymic tuft cell is a subset of terminally differentiated medullary thymic epithelial cell comprising 5-10% of total mTECs. Lineage-tracing studies indicate that this cell arises from mature MHCII mTECs, with development occurring through both Aire-dependent and Aire-independent pathways. However, its exact origins remain unclear."

  • database_cross_reference "PMID:30904566"

• Class: tuft cell of thymus

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

• tuft cell of thymus SubClassOf part of some medulla of thymus

• tuft cell of thymus SubClassOf capable of some antigen processing and presentation of endogenous peptide antigen via MHC class II

[aleixpuigb]

Please, see inline comments.

[Caroline-99]

#gogoeditdiff

[aleixpuigb]

Seeing this term it should be classified as 'professional antigen presenting cell', but that term needs changes (not all APCs are leukocytes. Therefore I approve this term and propose to revise that term ina different ticket