Fixes #2567 NTR - subepithelial intestinal fibroblast and two subclas…

…ses (#2591)

* Fixes #2567

Added subepithelial intestinal fibroblast and two subclasses

* Update cl-edit.owl

src/ontology/cl-edit.owl

@@ -3078,6 +3078,9 @@ Declaration(Class(obo:CL_4052003))
 Declaration(Class(obo:CL_4052004))
 Declaration(Class(obo:CL_4052005))
 Declaration(Class(obo:CL_4052006))
+Declaration(Class(obo:CL_4052007))
+Declaration(Class(obo:CL_4052008))
+Declaration(Class(obo:CL_4052009))
 Declaration(Class(obo:CL_4052048))
 Declaration(Class(obo:CL_4052049))
 Declaration(Class(obo:CP_0000000))
@@ -3201,6 +3204,7 @@ Declaration(Class(obo:UBERON_0011949))
 Declaration(Class(obo:UBERON_0012398))
 Declaration(Class(obo:UBERON_0012399))
 Declaration(Class(obo:UBERON_0012419))
+Declaration(Class(obo:UBERON_0013739))
 Declaration(Class(obo:UBERON_0014727))
 Declaration(Class(obo:UBERON_0014729))
 Declaration(Class(obo:UBERON_0027368))
@@ -32547,6 +32551,43 @@ SubClassOf(obo:CL_4052006 obo:CL_0011026)
 SubClassOf(obo:CL_4052006 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0011184))
 SubClassOf(obo:CL_4052006 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0002250))
 
+# Class: obo:CL_4052007 (subepithelial intestinal fibroblast)
+
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30270042") Annotation(oboInOwl:hasDbXref "PMID:33430285") Annotation(oboInOwl:hasDbXref "PMID:33916891") Annotation(oboInOwl:hasDbXref "PMID:37080817") obo:IAO_0000115 obo:CL_4052007 "A fibroblast located adjacent to the intestinal epithelium in both the small intestine and colon, specifically around the crypts. This cell is characterized by the expression of  PDGFRα and various collagen isoforms, including COL4A5 and COL4A6. It secretes signalling molecules like TGF-β, Wnt ligands, and BMPs, which are crucial for epithelial homeostasis, intestinal stem cell support, and basement membrane formation.")
+AnnotationAssertion(terms:contributor obo:CL_4052007 <https://orcid.org/0009-0000-8480-9277>)
+AnnotationAssertion(terms:date obo:CL_4052007 "2024-09-23T09:59:27Z"^^xsd:dateTime)
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30270042") Annotation(oboInOwl:hasDbXref "PMID:33916891") oboInOwl:hasRelatedSynonym obo:CL_4052007 "S2 fibroblast")
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33916891") oboInOwl:hasRelatedSynonym obo:CL_4052007 "S2 mesenchymal cells")
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30270042") Annotation(oboInOwl:hasDbXref "PMID:33916891") Annotation(oboInOwl:hasDbXref "PMID:37495570") rdfs:comment obo:CL_4052007 "The S2 fibroblast population has been identified as a subset of intestinal fibroblasts located near the epithelial lining. This population is divided into two subtypes: S2a and S2b. S2a is involved in epithelial differentiation, while S2b, located at the top of the crypt, regulates intestinal stem cell proliferation, niche formation, and wound healing.")
+AnnotationAssertion(rdfs:label obo:CL_4052007 "subepithelial intestinal fibroblast")
+SubClassOf(obo:CL_4052007 obo:CL_0000057)
+SubClassOf(obo:CL_4052007 ObjectSomeValuesFrom(obo:RO_0002220 obo:UBERON_0001277))
+
+# Class: obo:CL_4052008 (crypt-bottom fibroblast)
+
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33916891") Annotation(oboInOwl:hasDbXref "doi:/10.1371/journal.pbio.3001032") obo:IAO_0000115 obo:CL_4052008 "A subepithelial intestinal fibroblast that is located adjacent to the base of the crypt of Lieberkühn, near the intestinal stem cells. Characterized by low PDGFRα expression, this cell is crucial for maintaining the intestinal stem cell niche. Crypt-bottom fibroblast secretes key signaling molecules including canonical Wnt ligands (Wnt2, Wnt2b), Wnt potentiators (Rspo3), and BMP inhibitors (Grem1), which collectively regulate intestinal stem cell function and epithelial homeostasis.")
+AnnotationAssertion(terms:contributor obo:CL_4052008 <https://orcid.org/0009-0000-8480-9277>)
+AnnotationAssertion(terms:date obo:CL_4052008 "2024-09-23T10:23:18Z"^^xsd:dateTime)
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:/10.1371/journal.pbio.3001032") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4052008 "CBFs")
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33916891") oboInOwl:hasRelatedSynonym obo:CL_4052008 "bottom pericryptic-associated fibroblasts")
+AnnotationAssertion(rdfs:label obo:CL_4052008 "crypt-bottom fibroblast")
+SubClassOf(obo:CL_4052008 obo:CL_4052007)
+SubClassOf(obo:CL_4052008 ObjectSomeValuesFrom(obo:RO_0002220 obo:CL_0002250))
+SubClassOf(obo:CL_4052008 ObjectSomeValuesFrom(obo:RO_0002220 obo:UBERON_0013739))
+
+# Class: obo:CL_4052009 (crypt-top fibroblast)
+
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33916891") Annotation(oboInOwl:hasDbXref "doi:/10.1371/journal.pbio.3001032") obo:IAO_0000115 obo:CL_4052009 "A subepithelial intestinal fibroblast that is located adjacent to the top of the crypt of Lieberkuhn. Characterized by high experession of PDGFRα, this cell secretes a range of signaling factors, including WNTs and BMPs, that drive epithelial differentiation, creating a gradient that regulates the balance between stem cell maintenance and differentiation.")
+AnnotationAssertion(terms:contributor obo:CL_4052009 <https://orcid.org/0009-0000-8480-9277>)
+AnnotationAssertion(terms:date obo:CL_4052009 "2024-09-23T11:14:04Z"^^xsd:dateTime)
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:/10.1371/journal.pbio.3001032") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4052009 "CTFs")
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37495570") oboInOwl:hasRelatedSynonym obo:CL_4052009 "S2b fibroblast")
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33916891") oboInOwl:hasRelatedSynonym obo:CL_4052009 "top pericryptic fibroblast")
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37495570") rdfs:comment obo:CL_4052009 "S2b fibroblasts are located at the top of the crypt and express NRG1 and NPY.")
+AnnotationAssertion(rdfs:label obo:CL_4052009 "crypt-top fibroblast")
+SubClassOf(obo:CL_4052009 obo:CL_4052007)
+SubClassOf(obo:CL_4052009 ObjectSomeValuesFrom(obo:RO_0002220 obo:UBERON_0013740))
+
 # 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.")

src/ontology/imports/merged_import.owl

@@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/cl/imports/merged_import.owl>
-<http://purl.obolibrary.org/obo/cl/releases/2024-09-17/imports/merged_import.owl>
-Annotation(owl:versionInfo "2024-09-17")
+<http://purl.obolibrary.org/obo/cl/releases/2024-09-23/imports/merged_import.owl>
+Annotation(owl:versionInfo "2024-09-23")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000003>))
@@ -13090,6 +13090,12 @@ Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0013702>))
 Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0013703>))
 Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0013704>))
 Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0013727>))
+Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0013739>))
+Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0013740>))
+Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0013741>))
+Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0013742>))
+Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0013743>))
+Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0013744>))
 Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0013749>))
 Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0013750>))
 Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0013752>))
@@ -219296,6 +219302,72 @@ SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0013727> <http://purl.obolibra
 SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0013727> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0036242>))
 SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0013727> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0001025> <http://purl.obolibrary.org/obo/UBERON_0013704>))
 
+# Class: <http://purl.obolibrary.org/obo/UBERON_0013739> (base of crypt of Lieberkuhn)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "UBERON:md") Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "http://orcid.org/0000-0002-6601-2165") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/UBERON_0013739> "The basal portion (further from lumen) of an intestinal crypt. Contains multipotent stem cells. Stem cells in the crypts divide to form daughter cells. One daughter cell from each stem cell division is retained as a stem cell. The other becomes committed to differentiate along one of four pathways to become an enterocyte, enteroendocrine cell, goblet cell or Paneth cell.")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/UBERON_0013739> "basal portion of intestinal gland")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/UBERON_0013739> "base of intestinal gland")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/UBERON_0013739> "base part of epithelium of intestinal gland")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/UBERON_0013739> "uberon")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/UBERON_0013739> "UBERON:0013739")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0013739> "base of crypt of Lieberkuhn")
+EquivalentClasses(<http://purl.obolibrary.org/obo/UBERON_0013739> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/UBERON_0000483> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0001983>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002150> <http://purl.obolibrary.org/obo/UBERON_0013740>)))
+SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0013739> <http://purl.obolibrary.org/obo/UBERON_0011184>)
+SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0013739> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002150> <http://purl.obolibrary.org/obo/UBERON_0013740>))
+
+# Class: <http://purl.obolibrary.org/obo/UBERON_0013740> (wall of crypt of Lieberkuhn)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "UBERON:md") Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "http://orcid.org/0000-0002-6601-2165") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/UBERON_0013740> "The lateral parts of an intestinal crypt, continuous distally with the base and proximally with the intestinal villus epithelium.")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/UBERON_0013740> "wall of intestinal gland")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/UBERON_0013740> "wall part of epithelium of intestinal gland")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/UBERON_0013740> "uberon")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/UBERON_0013740> "UBERON:0013740")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0013740> "wall of crypt of Lieberkuhn")
+EquivalentClasses(<http://purl.obolibrary.org/obo/UBERON_0013740> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/UBERON_0000483> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0001983>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002150> <http://purl.obolibrary.org/obo/UBERON_0013739>)))
+SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0013740> <http://purl.obolibrary.org/obo/UBERON_0011184>)
+SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0013740> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002150> <http://purl.obolibrary.org/obo/UBERON_0013636>))
+SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0013740> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002150> <http://purl.obolibrary.org/obo/UBERON_0013739>))
+
+# Class: <http://purl.obolibrary.org/obo/UBERON_0013741> (base of crypt of Lieberkuhn of large intestine)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "OBOL:automatic") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/UBERON_0013741> "A base of crypt of Lieberkuhn that is part of a large intestine.")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/UBERON_0013741> "uberon")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/UBERON_0013741> "UBERON:0013741")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0013741> "base of crypt of Lieberkuhn of large intestine")
+EquivalentClasses(<http://purl.obolibrary.org/obo/UBERON_0013741> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/UBERON_0013739> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0000059>)))
+SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0013741> <http://purl.obolibrary.org/obo/UBERON_0001278>)
+SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0013741> <http://purl.obolibrary.org/obo/UBERON_0013739>)
+
+# Class: <http://purl.obolibrary.org/obo/UBERON_0013742> (wall of crypt of Lieberkuhn of large intestine)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "OBOL:automatic") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/UBERON_0013742> "A wall of crypt of Lieberkuhn that is part of a large intestine.")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/UBERON_0013742> "uberon")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/UBERON_0013742> "UBERON:0013742")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0013742> "wall of crypt of Lieberkuhn of large intestine")
+EquivalentClasses(<http://purl.obolibrary.org/obo/UBERON_0013742> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/UBERON_0013740> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0000059>)))
+SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0013742> <http://purl.obolibrary.org/obo/UBERON_0001278>)
+SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0013742> <http://purl.obolibrary.org/obo/UBERON_0013740>)
+
+# Class: <http://purl.obolibrary.org/obo/UBERON_0013743> (base of crypt of Lieberkuhn of small intestine)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "http://orcid.org/0000-0002-6601-2165") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/UBERON_0013743> "The basal portion (further from lumen) of a intestinal crypt that is located in the small intestine.")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/UBERON_0013743> "uberon")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/UBERON_0013743> "UBERON:0013743")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0013743> "base of crypt of Lieberkuhn of small intestine")
+EquivalentClasses(<http://purl.obolibrary.org/obo/UBERON_0013743> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/UBERON_0013739> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0002108>)))
+SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0013743> <http://purl.obolibrary.org/obo/UBERON_0001902>)
+SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0013743> <http://purl.obolibrary.org/obo/UBERON_0013739>)
+
+# Class: <http://purl.obolibrary.org/obo/UBERON_0013744> (wall of crypt of Lieberkuhn of small intestine)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "http://orcid.org/0000-0002-6601-2165") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/UBERON_0013744> "The lateral parts of an intestinal crypt that is located in the small intestine, continuous distally with the base and proximally with the intestinal villus epithelium.")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/UBERON_0013744> "uberon")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/UBERON_0013744> "UBERON:0013744")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0013744> "wall of crypt of Lieberkuhn of small intestine")
+EquivalentClasses(<http://purl.obolibrary.org/obo/UBERON_0013744> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/UBERON_0013740> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0002108>)))
+SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0013744> <http://purl.obolibrary.org/obo/UBERON_0001902>)
+SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0013744> <http://purl.obolibrary.org/obo/UBERON_0013740>)
+
 # Class: <http://purl.obolibrary.org/obo/UBERON_0013749> (metaphysis of humerus)
 
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "OBOL:automatic") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/UBERON_0013749> "A metaphysis that is part of a metaphysis.")

src/ontology/imports/uberon_terms.txt

@@ -53,4 +53,5 @@ UBERON:0004903
 UBERON:0004642
 UBERON:0006250
 UBERON:0014727
-UBERON:0014729
+UBERON:0014729
+UBERON:0013739

src/patterns/definitions.owl

@@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/cl/patterns/definitions.owl>
-<http://purl.obolibrary.org/obo/cl/releases/2024-09-17/patterns/definitions.owl>
-Annotation(owl:versionInfo "2024-09-17")
+<http://purl.obolibrary.org/obo/cl/releases/2024-09-23/patterns/definitions.owl>
+Annotation(owl:versionInfo "2024-09-23")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/CL_0000031>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CL_0000084>))