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Fixes #2903 tuft cell of nasal cavity #2918

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Fixes #2903 tuft cell of nasal cavity
Fixes #2903

Added a new term with textual and logical defs, synonyms and references
Caroline-99 committed Jan 21, 2025
commit 3cdca0aab7b0837c7a7be2ebbc062cd7b6e21259
33 changes: 22 additions & 11 deletions src/ontology/cl-edit.owl
Original file line number Diff line number Diff line change
@@ -3148,8 +3148,9 @@ Declaration(Class(obo:CL_4052029))
Declaration(Class(obo:CL_4052030))
Declaration(Class(obo:CL_4052031))
Declaration(Class(obo:CL_4052032))
Declaration(Class(obo:CL_4052035))
Declaration(Class(obo:CL_4052034))
Declaration(Class(obo:CL_4052035))
Declaration(Class(obo:CL_4052036))
Declaration(Class(obo:CL_4052048))
Declaration(Class(obo:CL_4052049))
Declaration(Class(obo:CP_0000000))
@@ -33530,6 +33531,18 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35389781") rdfs:comment
AnnotationAssertion(rdfs:label obo:CL_4052032 "granzyme H-associated CD8 T cell")
EquivalentClasses(obo:CL_4052032 ObjectIntersectionOf(obo:CL_0000909 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000003490)))

# Class: obo:CL_4052034 (tuft cell of thymus)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30904566") Annotation(oboInOwl:hasDbXref "PMID:35668088") Annotation(oboInOwl:hasDbXref "PMID:36351364") Annotation(oboInOwl:hasDbXref "PMID:36961668") obo:IAO_0000115 obo:CL_4052034 "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.")
AnnotationAssertion(terms:contributor obo:CL_4052034 <https://orcid.org/0009-0000-8480-9277>)
AnnotationAssertion(terms:date obo:CL_4052034 "2025-01-16T11:29:54Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30904566") oboInOwl:hasExactSynonym obo:CL_4052034 "thymic tuft cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30904566") rdfs:comment obo:CL_4052034 "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.")
AnnotationAssertion(rdfs:label obo:CL_4052034 "tuft cell of thymus")
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))

# Class: obo:CL_4052035 (tuft cell of pancreatic duct)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30904566") Annotation(oboInOwl:hasDbXref "PMID:32717220") obo:IAO_0000115 obo:CL_4052035 "A tuft cell that is part of the epithelium of pancreatic duct. Present in humans and rats, this cell is absent in the murine pancreas under normal conditions but emerges during acinar-to-ductal metaplasia triggered by injury, inflammation, or oncogenic mutations. It modulates the immune response and protects against pancreatic ductal adenocarcinoma progression by producing suppressive eicosanoids, such as prostaglandin D2. A tuft cell in the pancreatic duct highly expresses the transcription factor POU2F3, which is essential for its development and presence.")
@@ -33540,17 +33553,15 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32717220") oboInOwl:hasE
AnnotationAssertion(rdfs:label obo:CL_4052035 "tuft cell of pancreatic duct")
EquivalentClasses(obo:CL_4052035 ObjectIntersectionOf(obo:CL_0002204 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0009970)))

# Class: obo:CL_4052034 (tuft cell of thymus)
# Class: obo:CL_4052036 (tuft cell of nasal cavity)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30904566") Annotation(oboInOwl:hasDbXref "PMID:36961668") Annotation(oboInOwl:hasDbXref "PMID:35668088") Annotation(oboInOwl:hasDbXref "PMID:36351364") obo:IAO_0000115 obo:CL_4052034 "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.")
AnnotationAssertion(terms:contributor obo:CL_4052034 <https://orcid.org/0009-0000-8480-9277>)
AnnotationAssertion(terms:date obo:CL_4052034 "2025-01-16T11:29:54Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30904566") oboInOwl:hasExactSynonym obo:CL_4052034 "thymic tuft cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30904566") rdfs:comment obo:CL_4052034 "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.")
AnnotationAssertion(rdfs:label obo:CL_4052034 "tuft cell of thymus")
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.

AnnotationAssertion(terms:contributor obo:CL_4052036 <https://orcid.org/0009-0000-8480-9277>)
AnnotationAssertion(terms:date obo:CL_4052036 "2025-01-21T09:04:03Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34692913") oboInOwl:hasExactSynonym obo:CL_4052036 "nasal brush cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38306414") oboInOwl:hasExactSynonym obo:CL_4052036 "nasal tuft cell")
AnnotationAssertion(rdfs:label obo:CL_4052036 "tuft cell of nasal cavity")
EquivalentClasses(obo:CL_4052036 ObjectIntersectionOf(obo:CL_0002204 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0005384)))

# Class: obo:CL_4052048 (intercalated cell of salivary gland)