Fixes #2623 Fixes #2624 NTRs and revise classifications- fallopian tu…

…be epithelial cell and subclasses (#2631) * Fixes #2623 Fixes #2624 Fixes #2623 Fixes #2624 - Added two new terms - Revised the classification of fallopian tube epithelial cells - revised textual defs * Update cl-edit.owl
obophenotype · Oct 4, 2024 · 1764fe7 · 1764fe7
1 parent f96ced6
commit 1764fe7
Showing 1 changed file with 26 additions and 3 deletions.
diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl
@@ -3093,6 +3093,8 @@ Declaration(Class(obo:CL_4052010))
 Declaration(Class(obo:CL_4052011))
 Declaration(Class(obo:CL_4052012))
 Declaration(Class(obo:CL_4052013))
+Declaration(Class(obo:CL_4052018))
+Declaration(Class(obo:CL_4052019))
 Declaration(Class(obo:CL_4052048))
 Declaration(Class(obo:CL_4052049))
 Declaration(Class(obo:CP_0000000))
@@ -30744,19 +30746,20 @@ EquivalentClasses(obo:CL_4030005 ObjectIntersectionOf(obo:CL_0002201 ObjectSomeV
 
 # Class: obo:CL_4030006 (fallopian tube secretory epithelial cell)
 
-AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://doi.org/10.1186/1477-7827-7-129") Annotation(oboInOwl:hasDbXref "https://doi.org/10.3390/cells8080933") Annotation(oboInOwl:hasDbXref "https://www.proteinatlas.org/learn/dictionary/normal/fallopian+tube") obo:IAO_0000115 obo:CL_4030006 "An epithelial cell that is part of the fallopian tube epithelium that secretes mucous fluid and oviduct-specific products through the stimulation of estrogen and luteinizing hormone. The fallopian tube secretory cell has approximately the same height as the ciliated cell and is usually a more narrow columnar cell. The nucleus is ovoid and perpendicular to the long axis of the cell. The chromatin is more dense and the nucleolus smaller than that seen in the ciliated cell.")
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://doi.org/10.1186/1477-7827-7-129") Annotation(oboInOwl:hasDbXref "https://doi.org/10.3390/cells8080933") Annotation(oboInOwl:hasDbXref "https://www.proteinatlas.org/learn/dictionary/normal/fallopian+tube") obo:IAO_0000115 obo:CL_4030006 "An epithelial cell that is part of the fallopian tube that secretes mucus and oviduct-specific products in response to hormonal stimulation from estrogen and luteinizing hormone. This fallopian tube secretory cell is similar in height to the ciliated cell, but typically exhibits a more narrow, columnar shape. Its nucleus is ovoid and oriented perpendicular to the cell's long axis, with denser chromatin and a smaller nucleolus compared to the ciliated cell.")
 AnnotationAssertion(terms:contributor obo:CL_4030006 <https://orcid.org/0000-0002-0819-0473>)
 AnnotationAssertion(terms:date obo:CL_4030006 "2022-03-03T10:39:31Z"^^xsd:dateTime)
 AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_4030006 "oviduct secretory epithelial cell")
 AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4030006 "uterine tube secretory epithelial cell")
 AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://doi.org/10.1016/j.ccr.2013.10.013") Annotation(oboInOwl:hasDbXref "https://www.proteinatlas.org/learn/dictionary/normal/fallopian+tube") rdfs:comment obo:CL_4030006 "The other cell types of the fallopian tube epithelium include the ciliated cell and the intercalary cell, or peg cell. The fallopian tube secretory epithelial cell type has been implicated as a source of high-grade serous ovarian carcinoma.")
 AnnotationAssertion(rdfs:label obo:CL_4030006 "fallopian tube secretory epithelial cell")
 SubClassOf(obo:CL_4030006 obo:CL_1001591)
+SubClassOf(obo:CL_4030006 obo:CL_4052019)
 SubClassOf(obo:CL_4030006 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0003889))
 
 # Class: obo:CL_4030007 (fallopian tube ciliated cell)
 
-AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:16565155") obo:IAO_0000115 obo:CL_4030007 "An epithelial ciliated cell that is part of the fallopian tube. This cell type is found mainly on the apex of the mucosal folds and contributes, together with peristaltic contractions, to the self-propulsion of spermatozoa, the transport of ovum during ovulation and the transport of the fertilized ovum to the intramural fallopian tube. A fallopian tube ciliated cell has a columnar shape and contains an oval or round nucleus, often located perpendicular or parallel to the long axis of the cell.")
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:16565155") Annotation(oboInOwl:hasDbXref "https://www.proteinatlas.org/humanproteome/tissue/fallopian+tube") obo:IAO_0000115 obo:CL_4030007 "A multi-ciliated epithelial cell that is part of the fallopian tube, mainly found on the apex of the mucosal folds. This cell exhibits a columnar shape with an oval nucleus and is characterized by the presence of cilia on its surface. The coordinated beating of these cilia, together with peristaltic contractions, contributes to the self-propulsion of spermatozoa, the transport of ovum during ovulation and the transport of the fertilized ovum to the intramural fallopian tube.")
 AnnotationAssertion(terms:contributor obo:CL_4030007 <https://orcid.org/0000-0002-0819-0473>)
 AnnotationAssertion(terms:date obo:CL_4030007 "2022-03-08T12:40:19Z"^^xsd:dateTime)
 AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_4030007 "oviduct ciliated cell")
@@ -31490,7 +31493,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:22911892") oboInOwl:hasE
 AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:22911892") oboInOwl:hasExactSynonym obo:CL_4033014 "intercalary cell")
 AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:22911892") rdfs:comment obo:CL_4033014 "In vitro evidence supports a stem-cell/regenerative function for these cells")
 AnnotationAssertion(rdfs:label obo:CL_4033014 "peg cell")
-SubClassOf(obo:CL_4033014 obo:CL_0000066)
+SubClassOf(obo:CL_4033014 obo:CL_4052019)
 SubClassOf(obo:CL_4033014 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004804))
 
 # Class: obo:CL_4033015 (retinal astrocyte)
@@ -32755,6 +32758,26 @@ AnnotationAssertion(rdfs:label obo:CL_4052013 "externa theca cell")
 EquivalentClasses(obo:CL_4052013 ObjectIntersectionOf(obo:CL_0000503 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000156)))
 SubClassOf(obo:CL_4052013 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_4052010))
 
+# Class: obo:CL_4052018 (fallopian tube epithelial cell)
+
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "Wikipedia:Fallopian_tube") obo:IAO_0000115 obo:CL_4052018 "Any epithelial cell that is part of the fallopian tube.")
+AnnotationAssertion(terms:contributor obo:CL_4052018 <https://orcid.org/0009-0000-8480-9277>)
+AnnotationAssertion(terms:date obo:CL_4052018 "2024-10-01T12:09:12Z"^^xsd:dateTime)
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "Wikipedia:Fallopian_tube") oboInOwl:hasBroadSynonym obo:CL_4052018 "oviduct epithelial cell")
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "Wikipedia:Fallopian_tube") oboInOwl:hasExactSynonym obo:CL_4052018 "uterine tube epithelial cell")
+AnnotationAssertion(rdfs:label obo:CL_4052018 "fallopian tube epithelial cell")
+EquivalentClasses(obo:CL_4052018 ObjectIntersectionOf(obo:CL_0000066 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0003889)))
+
+# Class: obo:CL_4052019 (fallopian tube non-ciliated cell)
+
+AnnotationAssertion(obo:IAO_0000115 obo:CL_4052019 "Any epithelial cell that is part of the fallopian tube and lacks cilia.")
+AnnotationAssertion(terms:contributor obo:CL_4052019 <https://orcid.org/0009-0000-8480-9277>)
+AnnotationAssertion(terms:date obo:CL_4052019 "2024-10-01T12:12:12Z"^^xsd:dateTime)
+AnnotationAssertion(rdfs:label obo:CL_4052019 "fallopian tube non-ciliated cell")
+SubClassOf(obo:CL_4052019 obo:CL_0000066)
+SubClassOf(obo:CL_4052019 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0003889))
+SubClassOf(obo:CL_4052019 ObjectSomeValuesFrom(obo:CL_4030045 obo:GO_0005929))
+
 # 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.")