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Merge branch 'master' into 2702-dogiel-mesenteric-neurons
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@JABelfiore
JABelfiore committed Jan 31, 2025
2 parents ef0d49f + 1a6e403 commit c02afa1
Showing 1 changed file with 45 additions and 11 deletions.
56 changes: 45 additions & 11 deletions src/ontology/cl-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -3114,6 +3114,7 @@ Declaration(Class(obo:CL_4047032))
Declaration(Class(obo:CL_4047034))
Declaration(Class(obo:CL_4047035))
Declaration(Class(obo:CL_4047038))
Declaration(Class(obo:CL_4047040))
Declaration(Class(obo:CL_4047051))
Declaration(Class(obo:CL_4047052))
Declaration(Class(obo:CL_4047101))
Expand Down Expand Up @@ -3149,8 +3150,10 @@ 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_4052033))
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))
Expand Down Expand Up @@ -25166,9 +25169,11 @@ EquivalentClasses(obo:CL_1000272 ObjectIntersectionOf(obo:CL_0000151 ObjectSomeV

# Class: obo:CL_1000274 (trophectodermal cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:22918806") obo:IAO_0000115 obo:CL_1000274 "An extraembryonic cell that is part of the trophectoderm, representing the first lineage to differentiate in the embryo. This cell is crucial for implantation into the uterine wall and differentiates into trophoblast cells, which contribute to placenta formation and facilitate maternal-fetal nutrient and signal exchange.")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_1000274 "trophectoderm cell")
AnnotationAssertion(rdfs:label obo:CL_1000274 "trophectodermal cell")
SubClassOf(obo:CL_1000274 obo:CL_0000349)
EquivalentClasses(obo:CL_1000274 ObjectIntersectionOf(obo:CL_0000349 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004345)))
SubClassOf(obo:CL_1000274 ObjectSomeValuesFrom(obo:RO_0002203 obo:CL_0000351))

# Class: obo:CL_1000275 (smooth muscle cell of small intestine)

Expand Down Expand Up @@ -33146,6 +33151,15 @@ AnnotationAssertion(terms:date obo:CL_4047038 "2024-12-16T13:42:04Z"^^xsd:dateTi
AnnotationAssertion(rdfs:label obo:CL_4047038 "dogiel type I neuron")
SubClassOf(obo:CL_4047038 obo:CL_0000104)

# Class: obo:CL_4047040 (smooth muscle circular layer cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:18221249") Annotation(oboInOwl:hasDbXref "PMID:27445346") obo:IAO_0000115 obo:CL_4047040 "A smooth muscle cell that is found in the inner muscular layer of hollow organs. It is characterized by its spiral/helical arrangement around organ lumens. This cell is crucial for peristaltic movements in organs.")
AnnotationAssertion(terms:contributor obo:CL_4047040 <https://orcid.org/0009-0005-7919-4905>)
AnnotationAssertion(terms:date obo:CL_4047040 "2025-01-06T15:40:21Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:CL_4047040 "smooth muscle circular layer cell")
SubClassOf(obo:CL_4047040 obo:CL_0000192)
SubClassOf(obo:CL_4047040 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0012368))

# Class: obo:CL_4047051 (small intestine BEST4+ enterocyte)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:24223998") Annotation(oboInOwl:hasDbXref "PMID:34497389") obo:IAO_0000115 obo:CL_4047051 "An enterocyte of the human small intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels. These enterocytes have a disinctive transcriptomic profile and are scattered through the small intestine epithelium.")
Expand Down Expand Up @@ -33540,19 +33554,19 @@ 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_4052035 (tuft cell of pancreatic duct)
# Class: obo:CL_4052033 (biliary tuft cell)

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.")
AnnotationAssertion(terms:contributor obo:CL_4052035 <https://orcid.org/0009-0000-8480-9277>)
AnnotationAssertion(terms:date obo:CL_4052035 "2025-01-16T11:50:08Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:9749964") oboInOwl:hasExactSynonym obo:CL_4052035 "pancreatic brush cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32717220") oboInOwl:hasExactSynonym obo:CL_4052035 "pancreatic tuft cell")
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)))
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35245089") Annotation(oboInOwl:hasDbXref "PMID:37863104") obo:IAO_0000115 obo:CL_4052033 "A tuft cell that is part of the extrahepatic biliary tree, including the gallbladder and extrahepatic bile ducts. It shares a core genetic program with intestinal tuft cells but has unique tissue-specific genes. Biliary tuft cell functions as a bile acid-sensitive regulator, suppressing inflammation and modulating microbiome-dependent neutrophil infiltration in biliary tissues. Unlike its intestinal counterparts, this cell decreases in number postnatally as bile acid production matures, with its abundance negatively regulated by bile acids.")
AnnotationAssertion(terms:contributor obo:CL_4052033 <https://orcid.org/0009-0000-8480-9277>)
AnnotationAssertion(terms:date obo:CL_4052033 "2025-01-20T14:39:06Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35245089") oboInOwl:hasExactSynonym obo:CL_4052033 "gallbladder/extrahepatic bile duct tuft cell")
AnnotationAssertion(rdfs:label obo:CL_4052033 "biliary tuft cell")
SubClassOf(obo:CL_4052033 obo:CL_0002204)
SubClassOf(obo:CL_4052033 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0050728))

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

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(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")
Expand All @@ -33562,6 +33576,26 @@ EquivalentClasses(obo:CL_4052034 ObjectIntersectionOf(obo:CL_0002204 ObjectSomeV
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.")
AnnotationAssertion(terms:contributor obo:CL_4052035 <https://orcid.org/0009-0000-8480-9277>)
AnnotationAssertion(terms:date obo:CL_4052035 "2025-01-16T11:50:08Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:9749964") oboInOwl:hasExactSynonym obo:CL_4052035 "pancreatic brush cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32717220") oboInOwl:hasExactSynonym obo:CL_4052035 "pancreatic tuft cell")
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_4052036 (tuft cell of nasal cavity)

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. This cell plays key roles in chemosensation, lipid mediator production, immune responses, and epithelial homeostasis.")
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)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30855909") Annotation(oboInOwl:hasDbXref "PMID:35799078") Annotation(oboInOwl:hasDbXref "PMID:36726292") Annotation(oboInOwl:hasDbXref "PMID:37724716") obo:IAO_0000115 obo:CL_4052048 "A cuboidal epithelial cell that is part of the intercalated duct of salivary gland. This cell expresses proteins commonly associated with acinar cells and displays calcium signaling characteristics similar to secretory cells, indicating an active role in the secretory process rather than ion reabsorption.")
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