2562 ntrepithelial stem cell of gut #2601
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uberon term 0013739 imported
…com/obophenotype/cell-ontology into 2562-ntrepithelial-stem-cell-of-gut
…com/obophenotype/cell-ontology into 2562-ntrepithelial-stem-cell-of-gut
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#gogoeditdiff |
Here's a diff of how these changes impact the classified ontology (on -simple file):Ontology comparisonLeft
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Ontology importsOntology annotationsepithelial stem cell of gut
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Here's a diff of your edit file (unreasoned)Ontology comparisonLeft
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Ontology importsOntology annotationsbase of crypt of Lieberkuhn
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| # Class: obo:CL_4047020 (epithelial stem cell of gut) | ||
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| AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:24326621") Annotation(oboInOwl:hasDbXref "PMID:38835047") obo:IAO_0000115 obo:CL_4047020 "An epithelial stem cell located in a stem cell niche at the base of intestinal crypts. This cell is capable of self-renewal and multipotent differentiation into all intestinal epithelial cell types including enterocytes, goblet cells, enteroendocrine cells, and paneth cells. These cells divide rapidly to maintain epithelial homeostatis. A variety of adjacent cell types secrete signals that support and maintain the identity of this cell type in the niche, including Paneth Cells and specialised fibroblasts. | ||
| Expresses marker LGR5 in humans and markers ASCL2 and SMOC2 in mice.") |
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Can you please make sure that the core definition is one paragraph
| AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:24326621") oboInOwl:hasExactSynonym obo:CL_4047020 "IESCs") | ||
| AnnotationAssertion(rdfs:label obo:CL_4047020 "epithelial stem cell of gut"@en) | ||
| SubClassOf(obo:CL_4047020 obo:CL_0000036) | ||
| SubClassOf(obo:CL_4047020 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0013739)) |
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It has been inferred that epithelial stem cell of gut is a subclass of intestinal crypt stem cell (which is not accurate, as from my understanding, epithelial stem cell of gut should be the grouping/parent term. This inference is made because intestinal crypt stem cell is defined logically as any stem cell that is part of the crypt.
I am not sure if epithelial stem cell of gut term is needed as the existing term intestinal crypt stem cell also covers the base of the crypt and the functions described for "epithelial stem cells of gut" and "intestinal crypt stem cells" are essentially the same (have a look at the extended description for intestinal crypt stem cells). Both are responsible for the continuous renewal of the intestinal epithelium and can differentiate into all intestinal epithelial cell types. They also both refer to the same marker LGR5.
If you do decide to keep the term, make sure there is a clear differentiation in their definitions (ie. broad term 'epithelial stem cell of gut' with 'intestinal crypt stem cell' as a more specific subclass.
| Expresses marker LGR5 in humans and markers ASCL2 and SMOC2 in mice.") | ||
| AnnotationAssertion(terms:contributor obo:CL_4047020 <https://orcid.org/0009-0005-7919-4905>) | ||
| AnnotationAssertion(terms:date obo:CL_4047020 "2024-09-23T15:07:03Z"^^xsd:dateTime) | ||
| AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:24326621") oboInOwl:hasExactSynonym obo:CL_4047020 "IESCs") |
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does IESCs refer to Intestinal epithelial stem cells ? I couldn't find IESCs in PMID:24326621.
If you mean intestinal stem cell, you can use this reference PMID: 38835047.
| # Class: obo:CL_4047020 (epithelial stem cell of gut) | ||
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| AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:24326621") Annotation(oboInOwl:hasDbXref "PMID:38835047") obo:IAO_0000115 obo:CL_4047020 "An epithelial stem cell located in a stem cell niche at the base of intestinal crypts. This cell is capable of self-renewal and multipotent differentiation into all intestinal epithelial cell types including enterocytes, goblet cells, enteroendocrine cells, and paneth cells. These cells divide rapidly to maintain epithelial homeostatis. A variety of adjacent cell types secrete signals that support and maintain the identity of this cell type in the niche, including Paneth Cells and specialised fibroblasts. | ||
| Expresses marker LGR5 in humans and markers ASCL2 and SMOC2 in mice.") |
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I would suggest rewording the textual defs ie. An epithelial stem cell located at the base of intestinal crypts. This cell is capable of self-renewal and multipotent differentiation into all intestinal epithelial cell types including enterocytes, goblet cells, enteroendocrine cells, and paneth cells. It rapidly divides to maintain epithelial homeostasis and resides in a specialized niche supported by adjacent cell types, including Paneth cells and specialised fibroblasts. This cell epresses marker LGR5 in humans and markers ASCL2 and SMOC2 in mice.
| # Class: obo:CL_4047020 (epithelial stem cell of gut) | ||
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| AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:24326621") Annotation(oboInOwl:hasDbXref "PMID:38835047") obo:IAO_0000115 obo:CL_4047020 "An epithelial stem cell located in a stem cell niche at the base of intestinal crypts. This cell is capable of self-renewal and multipotent differentiation into all intestinal epithelial cell types including enterocytes, goblet cells, enteroendocrine cells, and paneth cells. These cells divide rapidly to maintain epithelial homeostatis. A variety of adjacent cell types secrete signals that support and maintain the identity of this cell type in the niche, including Paneth Cells and specialised fibroblasts. | ||
| Expresses marker LGR5 in humans and markers ASCL2 and SMOC2 in mice.") |
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It seems that LGR5 is not only expressed in humans but also in mice PMID: 32705632, PMID: 24326621
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@Caroline-99 Based on our discussions this morning lets leave this term for this round. |
Definition added