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obophenotype / cell-ontology

An ontology of cell types
https://obophenotype.github.io/cell-ontology/
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adjust-the-hierarchy-CNS-nematoda-and-CNS-vertebrata #2745

Closed AvolaAmg closed 1 week ago

AvolaAmg commented 2 weeks ago

Fixes #2654

AvolaAmg commented 2 weeks ago

gogoeditdiff

github-actions[bot] commented 2 weeks ago
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/2024-11-13/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/2024-11-13/cl-base.owl` - Loaded from: `file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl` ### Ontology imports ### Ontology annotations ### CNS neuron (sensu Nematoda and Protostomia) `http://purl.obolibrary.org/obo/CL_0000028` #### Removed - [CNS neuron (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000028) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) #### Added - [CNS neuron (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000028) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) ### CNS neuron (sensu Vertebrata) `http://purl.obolibrary.org/obo/CL_0000117` #### Removed - [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [neuroblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000031) - [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) - [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) #### Added - [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) ### anterior lateral line ganglion neuron `http://purl.obolibrary.org/obo/CL_0008021` #### Removed - [anterior lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_0008021) [IAO_0000115](http://purl.obolibrary.org/obo/IAO_0000115) "Any neuron that has its soma located in some anterior lateral line ganglion." - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated" - [anterior lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_0008021) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_2001391](http://purl.obolibrary.org/obo/UBERON_2001391)) #### Added - [anterior lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_0008021) [IAO_0000115](http://purl.obolibrary.org/obo/IAO_0000115) "Any peripheral nervous system neuron that has its soma located in some anterior lateral line ganglion." - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated" - [anterior lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_0008021) EquivalentTo [peripheral nervous system neuron](http://purl.obolibrary.org/obo/CL_2000032) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_2001391](http://purl.obolibrary.org/obo/UBERON_2001391)) ### columnar neuron `http://purl.obolibrary.org/obo/CL_0000112` #### Removed - [columnar neuron](http://purl.obolibrary.org/obo/CL_0000112) SubClassOf [RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [CNS neuron (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000028) - [columnar neuron](http://purl.obolibrary.org/obo/CL_0000112) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) #### Added - [columnar neuron](http://purl.obolibrary.org/obo/CL_0000112) SubClassOf [CNS neuron (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000028) ### immature neuron `http://purl.obolibrary.org/obo/CL_4042028` #### Removed - [immature neuron](http://purl.obolibrary.org/obo/CL_4042028) SubClassOf [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) #### Added - [immature neuron](http://purl.obolibrary.org/obo/CL_4042028) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) ### lateral line ganglion neuron `http://purl.obolibrary.org/obo/CL_2000031` #### Removed - [lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_2000031) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_2000120](http://purl.obolibrary.org/obo/UBERON_2000120)) - [lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_2000031) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) #### Added - [lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_2000031) EquivalentTo [peripheral nervous system neuron](http://purl.obolibrary.org/obo/CL_2000032) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_2000120](http://purl.obolibrary.org/obo/UBERON_2000120)) - [lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_2000031) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_32443](http://purl.obolibrary.org/obo/NCBITaxon_32443) - [lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_2000031) SubClassOf [peripheral nervous system neuron](http://purl.obolibrary.org/obo/CL_2000032) - [lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_2000031) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) ### posterior lateral line ganglion neuron `http://purl.obolibrary.org/obo/CL_1000245` #### Removed - [posterior lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_1000245) [IAO_0000115](http://purl.obolibrary.org/obo/IAO_0000115) "Any neuron that has its soma located in some posterior lateral line ganglion." - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated" - [posterior lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_1000245) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_2001314](http://purl.obolibrary.org/obo/UBERON_2001314)) #### Added - [posterior lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_1000245) [IAO_0000115](http://purl.obolibrary.org/obo/IAO_0000115) "Any peripheral nervous system neuron that has its soma located in some posterior lateral line ganglion." - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated" - [posterior lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_1000245) EquivalentTo [peripheral nervous system neuron](http://purl.obolibrary.org/obo/CL_2000032) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_2001314](http://purl.obolibrary.org/obo/UBERON_2001314)) ### primary interneuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000534` #### Removed - [primary interneuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000534) SubClassOf [interneuron](http://purl.obolibrary.org/obo/CL_0000099) #### Added - [primary interneuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000534) SubClassOf [CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) ### primary neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000530` #### Removed - [primary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000530) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) #### Added - [primary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000530) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) ### secondary neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000535` #### Removed - [secondary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000535) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) #### Added - [secondary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000535) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029)
github-actions[bot] commented 2 weeks ago
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 ### CNS neuron (sensu Nematoda and Protostomia) `http://purl.obolibrary.org/obo/CL_0000028` #### Removed - [CNS neuron (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000028) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) #### Added - [CNS neuron (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000028) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) ### CNS neuron (sensu Vertebrata) `http://purl.obolibrary.org/obo/CL_0000117` #### Removed - [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [neuroblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000031) - [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) #### Added - [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) ### anterior lateral line ganglion neuron `http://purl.obolibrary.org/obo/CL_0008021` #### Removed - [anterior lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_0008021) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([has soma location](http://purl.obolibrary.org/obo/RO_0002100) some [anterior lateral line ganglion](http://purl.obolibrary.org/obo/UBERON_2001391)) #### Added - [anterior lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_0008021) EquivalentTo [peripheral nervous system neuron](http://purl.obolibrary.org/obo/CL_2000032) and ([has soma location](http://purl.obolibrary.org/obo/RO_0002100) some [anterior lateral line ganglion](http://purl.obolibrary.org/obo/UBERON_2001391)) ### columnar neuron `http://purl.obolibrary.org/obo/CL_0000112` #### Removed - [columnar neuron](http://purl.obolibrary.org/obo/CL_0000112) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) - [columnar neuron](http://purl.obolibrary.org/obo/CL_0000112) SubClassOf [has soma location](http://purl.obolibrary.org/obo/RO_0002100) some [CNS neuron (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000028) #### Added - [columnar neuron](http://purl.obolibrary.org/obo/CL_0000112) SubClassOf [CNS neuron (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000028) - [columnar neuron](http://purl.obolibrary.org/obo/CL_0000112) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [neuroblast (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000338) - [columnar neuron](http://purl.obolibrary.org/obo/CL_0000112) SubClassOf [has soma location](http://purl.obolibrary.org/obo/RO_0002100) some [central nervous system](http://purl.obolibrary.org/obo/UBERON_0001017) ### immature neuron `http://purl.obolibrary.org/obo/CL_4042028` #### Removed - [immature neuron](http://purl.obolibrary.org/obo/CL_4042028) SubClassOf [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) #### Added - [immature neuron](http://purl.obolibrary.org/obo/CL_4042028) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) ### lateral line ganglion neuron `http://purl.obolibrary.org/obo/CL_2000031` #### Removed - [lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_2000031) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([has soma location](http://purl.obolibrary.org/obo/RO_0002100) some [lateral line ganglion](http://purl.obolibrary.org/obo/UBERON_2000120)) #### Added - [lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_2000031) EquivalentTo [peripheral nervous system neuron](http://purl.obolibrary.org/obo/CL_2000032) and ([has soma location](http://purl.obolibrary.org/obo/RO_0002100) some [lateral line ganglion](http://purl.obolibrary.org/obo/UBERON_2000120)) - [lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_2000031) SubClassOf [in taxon](http://purl.obolibrary.org/obo/RO_0002162) some [Teleostei](http://purl.obolibrary.org/obo/NCBITaxon_32443) ### posterior lateral line ganglion neuron `http://purl.obolibrary.org/obo/CL_1000245` #### Removed - [posterior lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_1000245) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([has soma location](http://purl.obolibrary.org/obo/RO_0002100) some [posterior lateral line ganglion](http://purl.obolibrary.org/obo/UBERON_2001314)) #### Added - [posterior lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_1000245) EquivalentTo [peripheral nervous system neuron](http://purl.obolibrary.org/obo/CL_2000032) and ([has soma location](http://purl.obolibrary.org/obo/RO_0002100) some [posterior lateral line ganglion](http://purl.obolibrary.org/obo/UBERON_2001314)) ### primary neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000530` #### Added - [primary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000530) SubClassOf [has soma location](http://purl.obolibrary.org/obo/RO_0002100) some [central nervous system](http://purl.obolibrary.org/obo/UBERON_0001017) ### secondary neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000535` #### Added - [secondary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000535) SubClassOf [has soma location](http://purl.obolibrary.org/obo/RO_0002100) some [central nervous system](http://purl.obolibrary.org/obo/UBERON_0001017)
AvolaAmg commented 1 week ago

gogoeditdiff