Fixes #2675 Added developmental lineages for intestinal epithelial cells

[Caroline-99]

• Added developmental lineages for intestinal epithelial cells + added references to support the new logical axiom
• Revised logical defs of paneth cell

Note: I have specified that intestinal tuft cells develop from some intestinal crypt stem cell rather than transit amplifying cells of the gut because I could not find direct support indicating that TA cells are involved in their development. The literature suggests that tuft cells originate from LGR5+ crypt base columnar stem cells (intestinal crypt stem cell) but may also follow a distinct developmental pathway (ie.self renew).

[Caroline-99]

gogoeditdiff

[github-actions[bot]]

Here's a diff of how these changes impact the classified ontology (on -base file):

# Ontology comparison ## Left - Ontology IRI: `http://purl.obolibrary.org/obo/cl/cl-base.owl` - Version IRI: `http://purl.obolibrary.org/obo/cl/releases/2024-11-28/cl-base.owl` - Loaded from: `file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-master.owl/cl-base.owl` ## Right - Ontology IRI: `http://purl.obolibrary.org/obo/cl/cl-base.owl` - Version IRI: `http://purl.obolibrary.org/obo/cl/releases/2024-11-28/cl-base.owl` - Loaded from: `file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl` ### Ontology imports ### Ontology annotations ### enterocyte `http://purl.obolibrary.org/obo/CL_0000584` #### Added - [enterocyte](http://purl.obolibrary.org/obo/CL_0000584) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [early enterocyte](http://purl.obolibrary.org/obo/CL_4047019) ### intestinal enteroendocrine cell `http://purl.obolibrary.org/obo/CL_1001516` #### Added - [intestinal enteroendocrine cell](http://purl.obolibrary.org/obo/CL_1001516) SubClassOf [RO_0002207](http://purl.obolibrary.org/obo/RO_0002207) some [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) ### intestinal tuft cell `http://purl.obolibrary.org/obo/CL_0019032` #### Removed - [intestinal tuft cell](http://purl.obolibrary.org/obo/CL_0019032) [IAO_0000115](http://purl.obolibrary.org/obo/IAO_0000115) "Any brush cell that is part of the intestinal epithelium." - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:22527717" #### Added - [intestinal tuft cell](http://purl.obolibrary.org/obo/CL_0019032) [IAO_0000115](http://purl.obolibrary.org/obo/IAO_0000115) "Any brush cell that is part of the intestinal epithelium." - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:39358509" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:22527717" - [intestinal tuft cell](http://purl.obolibrary.org/obo/CL_0019032) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [intestinal crypt stem cell](http://purl.obolibrary.org/obo/CL_0002250) ### intestine goblet cell `http://purl.obolibrary.org/obo/CL_0019031` #### Removed - [intestine goblet cell](http://purl.obolibrary.org/obo/CL_0019031) [IAO_0000115](http://purl.obolibrary.org/obo/IAO_0000115) "Goblet cells reside throughout the length of the small and large intestine and are responsible for the production and maintenance of the protective mucus blanket by synthesizing and secreting high-molecular-weight glycoproteins known as mucins. Human intestinal goblet cells secrete the MUC2 mucin, as well as a number of typical mucus components: CLCA1, FCGBP, AGR2, ZG16, and TFF3." - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:1996606" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:24942678" #### Added - [intestine goblet cell](http://purl.obolibrary.org/obo/CL_0019031) [IAO_0000115](http://purl.obolibrary.org/obo/IAO_0000115) "Goblet cells reside throughout the length of the small and large intestine and are responsible for the production and maintenance of the protective mucus blanket by synthesizing and secreting high-molecular-weight glycoproteins known as mucins. Human intestinal goblet cells secrete the MUC2 mucin, as well as a number of typical mucus components: CLCA1, FCGBP, AGR2, ZG16, and TFF3." - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:1996606" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:24942678" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33484640" - [intestine goblet cell](http://purl.obolibrary.org/obo/CL_0019031) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [transit amplifying cell of gut](http://purl.obolibrary.org/obo/CL_4047017) ### paneth cell `http://purl.obolibrary.org/obo/CL_0000510` #### Removed - [paneth cell](http://purl.obolibrary.org/obo/CL_0000510) [IAO_0000115](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell found in the basal part of the intestinal glands (crypts of Lieberkuhn) including the appendix. Paneth cells synthesize and secrete lysozyme and cryptdins. Numerous in the deeper parts of the intestinal crypts, particularly in the duodenum, rich in zinc, contain large acidophilic granules, with irregular apical microvilli and prominent membrane-bound vacuoles containing matrix." - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0517223651" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29184701" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D019879" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32308658" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm" - [paneth cell](http://purl.obolibrary.org/obo/CL_0000510) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001983](http://purl.obolibrary.org/obo/UBERON_0001983) #### Added - [paneth cell](http://purl.obolibrary.org/obo/CL_0000510) [IAO_0000115](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell found in the basal part of the intestinal glands (crypts of Lieberkuhn) including the appendix. Paneth cells synthesize and secrete lysozyme and cryptdins. Numerous in the deeper parts of the intestinal crypts, particularly in the duodenum, rich in zinc, contain large acidophilic granules, with irregular apical microvilli and prominent membrane-bound vacuoles containing matrix." - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0517223651" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29184701" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D019879" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32308658" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33484640" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm" - [paneth cell](http://purl.obolibrary.org/obo/CL_0000510) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [transit amplifying cell of gut](http://purl.obolibrary.org/obo/CL_4047017) - [paneth cell](http://purl.obolibrary.org/obo/CL_0000510) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0011184](http://purl.obolibrary.org/obo/UBERON_0011184)

[github-actions[bot]]

Here's a diff of your edit file (unreasoned)

# Ontology comparison ## Left - Ontology IRI: `http://purl.obolibrary.org/obo/cl.owl` - Version IRI: *None* - Loaded from: `file:/__w/cell-ontology/cell-ontology/master/src/ontology/cl-edit.owl` ## Right - Ontology IRI: `http://purl.obolibrary.org/obo/cl.owl` - Version IRI: *None* - Loaded from: `file:/__w/cell-ontology/cell-ontology/branch/src/ontology/cl-edit.owl` ### Ontology imports ### Ontology annotations ### enterocyte `http://purl.obolibrary.org/obo/CL_0000584` #### Added - [enterocyte](http://purl.obolibrary.org/obo/CL_0000584) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [early enterocyte](http://purl.obolibrary.org/obo/CL_4047019) ### intestinal enteroendocrine cell `http://purl.obolibrary.org/obo/CL_1001516` #### Added - [intestinal enteroendocrine cell](http://purl.obolibrary.org/obo/CL_1001516) SubClassOf [directly develops from](http://purl.obolibrary.org/obo/RO_0002207) some [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) ### intestinal tuft cell `http://purl.obolibrary.org/obo/CL_0019032` #### Removed - [intestinal tuft cell](http://purl.obolibrary.org/obo/CL_0019032) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any brush cell that is part of the intestinal epithelium." - [has cross-reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:22527717" #### Added - [intestinal tuft cell](http://purl.obolibrary.org/obo/CL_0019032) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any brush cell that is part of the intestinal epithelium." - [has cross-reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:22527717" - [has cross-reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:39358509" - [intestinal tuft cell](http://purl.obolibrary.org/obo/CL_0019032) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [intestinal crypt stem cell](http://purl.obolibrary.org/obo/CL_0002250) ### intestine goblet cell `http://purl.obolibrary.org/obo/CL_0019031` #### Removed - [intestine goblet cell](http://purl.obolibrary.org/obo/CL_0019031) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Goblet cells reside throughout the length of the small and large intestine and are responsible for the production and maintenance of the protective mucus blanket by synthesizing and secreting high-molecular-weight glycoproteins known as mucins. Human intestinal goblet cells secrete the MUC2 mucin, as well as a number of typical mucus components: CLCA1, FCGBP, AGR2, ZG16, and TFF3." - [has cross-reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:24942678" - [has cross-reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:1996606" #### Added - [intestine goblet cell](http://purl.obolibrary.org/obo/CL_0019031) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Goblet cells reside throughout the length of the small and large intestine and are responsible for the production and maintenance of the protective mucus blanket by synthesizing and secreting high-molecular-weight glycoproteins known as mucins. Human intestinal goblet cells secrete the MUC2 mucin, as well as a number of typical mucus components: CLCA1, FCGBP, AGR2, ZG16, and TFF3." - [has cross-reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33484640" - [has cross-reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:24942678" - [has cross-reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:1996606" - [intestine goblet cell](http://purl.obolibrary.org/obo/CL_0019031) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [transit amplifying cell of gut](http://purl.obolibrary.org/obo/CL_4047017) ### paneth cell `http://purl.obolibrary.org/obo/CL_0000510` #### Removed - [paneth cell](http://purl.obolibrary.org/obo/CL_0000510) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell found in the basal part of the intestinal glands (crypts of Lieberkuhn) including the appendix. Paneth cells synthesize and secrete lysozyme and cryptdins. Numerous in the deeper parts of the intestinal crypts, particularly in the duodenum, rich in zinc, contain large acidophilic granules, with irregular apical microvilli and prominent membrane-bound vacuoles containing matrix." - [has cross-reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32308658" - [has cross-reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0517223651" - [has cross-reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29184701" - [has cross-reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D019879" - [has cross-reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm" - [paneth cell](http://purl.obolibrary.org/obo/CL_0000510) SubClassOf [part of](http://purl.obolibrary.org/obo/BFO_0000050) some [intestinal epithelium](http://purl.obolibrary.org/obo/UBERON_0001277) - [paneth cell](http://purl.obolibrary.org/obo/CL_0000510) SubClassOf [part of](http://purl.obolibrary.org/obo/BFO_0000050) some [crypt of Lieberkuhn](http://purl.obolibrary.org/obo/UBERON_0001983) #### Added - [paneth cell](http://purl.obolibrary.org/obo/CL_0000510) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell found in the basal part of the intestinal glands (crypts of Lieberkuhn) including the appendix. Paneth cells synthesize and secrete lysozyme and cryptdins. Numerous in the deeper parts of the intestinal crypts, particularly in the duodenum, rich in zinc, contain large acidophilic granules, with irregular apical microvilli and prominent membrane-bound vacuoles containing matrix." - [has cross-reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33484640" - [has cross-reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32308658" - [has cross-reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0517223651" - [has cross-reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29184701" - [has cross-reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D019879" - [has cross-reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm" - [paneth cell](http://purl.obolibrary.org/obo/CL_0000510) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [transit amplifying cell of gut](http://purl.obolibrary.org/obo/CL_4047017) - [paneth cell](http://purl.obolibrary.org/obo/CL_0000510) SubClassOf [part of](http://purl.obolibrary.org/obo/BFO_0000050) some [epithelium of crypt of Lieberkuhn](http://purl.obolibrary.org/obo/UBERON_0011184)

[dosumis]

gogoeditdiff