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obophenotype / cell-ontology

An ontology of cell types
https://obophenotype.github.io/cell-ontology/
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Fixing lung multiciliated cell heirarchy #2735

Closed dosumis closed 2 weeks ago

dosumis commented 2 weeks ago

Fixed by aligning both textual and logical defs Fixes #432 Note - classification of "bronchus ciliated cell" under lung will be fixed by https://github.com/obophenotype/uberon/issues/3410

dosumis 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/2024-11-08/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/2024-11-08/cl-base.owl` - Loaded from: `file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl` ### Ontology imports ### Ontology annotations ### airway submucosal gland duct ciliated cell `http://purl.obolibrary.org/obo/CL_4033055` #### Removed - [airway submucosal gland duct ciliated cell](http://purl.obolibrary.org/obo/CL_4033055) [IAO_0000115](http://purl.obolibrary.org/obo/IAO_0000115) "A ciliated cell that is part of a ciliated duct of an airway submucosal gland." - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30864819" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:17707699" - [airway submucosal gland duct ciliated cell](http://purl.obolibrary.org/obo/CL_4033055) EquivalentTo [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_8410077](http://purl.obolibrary.org/obo/UBERON_8410077)) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_8600014](http://purl.obolibrary.org/obo/UBERON_8600014)) - [airway submucosal gland duct ciliated cell](http://purl.obolibrary.org/obo/CL_4033055) SubClassOf [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) #### Added - [airway submucosal gland duct ciliated cell](http://purl.obolibrary.org/obo/CL_4033055) [IAO_0000115](http://purl.obolibrary.org/obo/IAO_0000115) "A multi-ciliated epithelial cell located in ciliated duct of an airway submucosal gland, characterized by a columnar shape and motile cilia on its apical surface." - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30864819" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:17707699" - [airway submucosal gland duct ciliated cell](http://purl.obolibrary.org/obo/CL_4033055) EquivalentTo [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_8410077](http://purl.obolibrary.org/obo/UBERON_8410077)) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_8600014](http://purl.obolibrary.org/obo/UBERON_8600014)) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0031514](http://purl.obolibrary.org/obo/GO_0031514)) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0010007](http://purl.obolibrary.org/obo/PATO_0010007)) - [airway submucosal gland duct ciliated cell](http://purl.obolibrary.org/obo/CL_4033055) SubClassOf [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) - [airway submucosal gland duct ciliated cell](http://purl.obolibrary.org/obo/CL_4033055) SubClassOf [duct epithelial cell](http://purl.obolibrary.org/obo/CL_0000068) ### ciliated cell of the bronchus `http://purl.obolibrary.org/obo/CL_0002332` #### Removed - [ciliated cell of the bronchus](http://purl.obolibrary.org/obo/CL_0002332) [IAO_0000115](http://purl.obolibrary.org/obo/IAO_0000115) "A ciliated cell of the bronchus." - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:18757316" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm" - [ciliated cell of the bronchus](http://purl.obolibrary.org/obo/CL_0002332) EquivalentTo [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002031](http://purl.obolibrary.org/obo/UBERON_0002031)) #### Added - [ciliated cell of the bronchus](http://purl.obolibrary.org/obo/CL_0002332) [IAO_0000115](http://purl.obolibrary.org/obo/IAO_0000115) "A multi-ciliated epithelial cell located in the bronchus epithelium, characterized by a columnar shape and motile cilia on its apical surface." - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:18757316" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm" - [ciliated cell of the bronchus](http://purl.obolibrary.org/obo/CL_0002332) EquivalentTo [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002031](http://purl.obolibrary.org/obo/UBERON_0002031)) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0031514](http://purl.obolibrary.org/obo/GO_0031514)) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0010007](http://purl.obolibrary.org/obo/PATO_0010007)) ### ciliated columnar cell of tracheobronchial tree `http://purl.obolibrary.org/obo/CL_0002145` #### Removed - [ciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) SubClassOf [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) #### Added - [ciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) EquivalentTo [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0008397](http://purl.obolibrary.org/obo/UBERON_0008397)) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0031514](http://purl.obolibrary.org/obo/GO_0031514)) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0010007](http://purl.obolibrary.org/obo/PATO_0010007)) ### lung ciliated cell `http://purl.obolibrary.org/obo/CL_1000271` #### Removed - [lung ciliated cell](http://purl.obolibrary.org/obo/CL_1000271) EquivalentTo [ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0000067) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000115](http://purl.obolibrary.org/obo/UBERON_0000115)) - [lung ciliated cell](http://purl.obolibrary.org/obo/CL_1000271) SubClassOf [ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0000067) #### Added - [lung ciliated cell](http://purl.obolibrary.org/obo/CL_1000271) EquivalentTo [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000115](http://purl.obolibrary.org/obo/UBERON_0000115)) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0031514](http://purl.obolibrary.org/obo/GO_0031514)) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0010007](http://purl.obolibrary.org/obo/PATO_0010007)) ### respiratory ciliated cell `http://purl.obolibrary.org/obo/CL_4030034` #### Removed - [respiratory ciliated cell](http://purl.obolibrary.org/obo/CL_4030034) [IAO_0000115](http://purl.obolibrary.org/obo/IAO_0000115) "A ciliated cell of the respiratory system. Ciliated cells are present in airway epithelium." - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:18757316" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:21364219" - [respiratory ciliated cell](http://purl.obolibrary.org/obo/CL_4030034) EquivalentTo [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004802](http://purl.obolibrary.org/obo/UBERON_0004802)) - [respiratory ciliated cell](http://purl.obolibrary.org/obo/CL_4030034) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004802](http://purl.obolibrary.org/obo/UBERON_0004802) - [respiratory ciliated cell](http://purl.obolibrary.org/obo/CL_4030034) SubClassOf [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) #### Added - [respiratory ciliated cell](http://purl.obolibrary.org/obo/CL_4030034) [IAO_0000115](http://purl.obolibrary.org/obo/IAO_0000115) "A multi-ciliated epithelial cell located in the respiratory tract epithelium, characterized by a columnar shape and motile cilia on its apical surface." - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:18757316" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:21364219" - [respiratory ciliated cell](http://purl.obolibrary.org/obo/CL_4030034) EquivalentTo [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004802](http://purl.obolibrary.org/obo/UBERON_0004802)) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0031514](http://purl.obolibrary.org/obo/GO_0031514)) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0010007](http://purl.obolibrary.org/obo/PATO_0010007)) - [respiratory ciliated cell](http://purl.obolibrary.org/obo/CL_4030034) SubClassOf [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) - [respiratory ciliated cell](http://purl.obolibrary.org/obo/CL_4030034) SubClassOf [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368)
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 ### airway submucosal gland duct ciliated cell `http://purl.obolibrary.org/obo/CL_4033055` #### Removed - [airway submucosal gland duct ciliated cell](http://purl.obolibrary.org/obo/CL_4033055) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A ciliated cell that is part of a ciliated duct of an airway submucosal gland." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30864819" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:17707699" - [airway submucosal gland duct ciliated cell](http://purl.obolibrary.org/obo/CL_4033055) EquivalentTo [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) and ([part of](http://purl.obolibrary.org/obo/BFO_0000050) some [airway submucosal gland](http://purl.obolibrary.org/obo/UBERON_8410077)) and ([part of](http://purl.obolibrary.org/obo/BFO_0000050) some [submucosal gland ciliated duct](http://purl.obolibrary.org/obo/UBERON_8600014)) #### Added - [airway submucosal gland duct ciliated cell](http://purl.obolibrary.org/obo/CL_4033055) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A multi-ciliated epithelial cell located in ciliated duct of an airway submucosal gland, characterized by a columnar shape and motile cilia on its apical surface." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30864819" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:17707699" - [airway submucosal gland duct ciliated cell](http://purl.obolibrary.org/obo/CL_4033055) EquivalentTo [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) and ([part of](http://purl.obolibrary.org/obo/BFO_0000050) some [airway submucosal gland](http://purl.obolibrary.org/obo/UBERON_8410077)) and ([part of](http://purl.obolibrary.org/obo/BFO_0000050) some [submucosal gland ciliated duct](http://purl.obolibrary.org/obo/UBERON_8600014)) and ([has part](http://purl.obolibrary.org/obo/BFO_0000051) some [motile cilium](http://purl.obolibrary.org/obo/GO_0031514)) and ([bearer of](http://purl.obolibrary.org/obo/RO_0000053) some [multiciliated](http://purl.obolibrary.org/obo/PATO_0010007)) ### ciliated cell of the bronchus `http://purl.obolibrary.org/obo/CL_0002332` #### Removed - [ciliated cell of the bronchus](http://purl.obolibrary.org/obo/CL_0002332) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A ciliated cell of the bronchus." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:18757316" - [ciliated cell of the bronchus](http://purl.obolibrary.org/obo/CL_0002332) EquivalentTo [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) and ([part of](http://purl.obolibrary.org/obo/BFO_0000050) some [epithelium of bronchus](http://purl.obolibrary.org/obo/UBERON_0002031)) - [ciliated cell of the bronchus](http://purl.obolibrary.org/obo/CL_0002332) SubClassOf [ciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) #### Added - [ciliated cell of the bronchus](http://purl.obolibrary.org/obo/CL_0002332) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A multi-ciliated epithelial cell located in the bronchus epithelium, characterized by a columnar shape and motile cilia on its apical surface." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:18757316" - [ciliated cell of the bronchus](http://purl.obolibrary.org/obo/CL_0002332) EquivalentTo [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) and ([part of](http://purl.obolibrary.org/obo/BFO_0000050) some [epithelium of bronchus](http://purl.obolibrary.org/obo/UBERON_0002031)) and ([has part](http://purl.obolibrary.org/obo/BFO_0000051) some [motile cilium](http://purl.obolibrary.org/obo/GO_0031514)) and ([bearer of](http://purl.obolibrary.org/obo/RO_0000053) some [multiciliated](http://purl.obolibrary.org/obo/PATO_0010007)) ### ciliated columnar cell of tracheobronchial tree `http://purl.obolibrary.org/obo/CL_0002145` #### Removed - [ciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) SubClassOf [respiratory ciliated cell](http://purl.obolibrary.org/obo/CL_4030034) - [ciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) SubClassOf [has part](http://purl.obolibrary.org/obo/BFO_0000051) some [motile cilium](http://purl.obolibrary.org/obo/GO_0031514) - [ciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) SubClassOf [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) - [ciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) SubClassOf [epithelial cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002202) #### Added - [ciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) EquivalentTo [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) and ([part of](http://purl.obolibrary.org/obo/BFO_0000050) some [tracheobronchial epithelium](http://purl.obolibrary.org/obo/UBERON_0008397)) and ([has part](http://purl.obolibrary.org/obo/BFO_0000051) some [motile cilium](http://purl.obolibrary.org/obo/GO_0031514)) and ([bearer of](http://purl.obolibrary.org/obo/RO_0000053) some [multiciliated](http://purl.obolibrary.org/obo/PATO_0010007)) ### lung ciliated cell `http://purl.obolibrary.org/obo/CL_1000271` #### Removed - [lung ciliated cell](http://purl.obolibrary.org/obo/CL_1000271) EquivalentTo [ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0000067) and ([part of](http://purl.obolibrary.org/obo/BFO_0000050) some [lung epithelium](http://purl.obolibrary.org/obo/UBERON_0000115)) #### Added - [lung ciliated cell](http://purl.obolibrary.org/obo/CL_1000271) EquivalentTo [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) and ([part of](http://purl.obolibrary.org/obo/BFO_0000050) some [lung epithelium](http://purl.obolibrary.org/obo/UBERON_0000115)) and ([has part](http://purl.obolibrary.org/obo/BFO_0000051) some [motile cilium](http://purl.obolibrary.org/obo/GO_0031514)) and ([bearer of](http://purl.obolibrary.org/obo/RO_0000053) some [multiciliated](http://purl.obolibrary.org/obo/PATO_0010007)) ### respiratory ciliated cell `http://purl.obolibrary.org/obo/CL_4030034` #### Removed - [respiratory ciliated cell](http://purl.obolibrary.org/obo/CL_4030034) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A ciliated cell of the respiratory system. Ciliated cells are present in airway epithelium." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:21364219" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:18757316" - [respiratory ciliated cell](http://purl.obolibrary.org/obo/CL_4030034) EquivalentTo [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) and ([part of](http://purl.obolibrary.org/obo/BFO_0000050) some [respiratory tract epithelium](http://purl.obolibrary.org/obo/UBERON_0004802)) - [respiratory ciliated cell](http://purl.obolibrary.org/obo/CL_4030034) SubClassOf [part of](http://purl.obolibrary.org/obo/BFO_0000050) some [respiratory system](http://purl.obolibrary.org/obo/UBERON_0001004) #### Added - [respiratory ciliated cell](http://purl.obolibrary.org/obo/CL_4030034) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A multi-ciliated epithelial cell located in the respiratory tract epithelium, characterized by a columnar shape and motile cilia on its apical surface." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:21364219" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:18757316" - [respiratory ciliated cell](http://purl.obolibrary.org/obo/CL_4030034) EquivalentTo [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) and ([part of](http://purl.obolibrary.org/obo/BFO_0000050) some [respiratory tract epithelium](http://purl.obolibrary.org/obo/UBERON_0004802)) and ([has part](http://purl.obolibrary.org/obo/BFO_0000051) some [motile cilium](http://purl.obolibrary.org/obo/GO_0031514)) and ([bearer of](http://purl.obolibrary.org/obo/RO_0000053) some [multiciliated](http://purl.obolibrary.org/obo/PATO_0010007)) ### sensory processing `http://purl.obolibrary.org/obo/GO_0050893` #### Added - Class: [sensory processing](http://purl.obolibrary.org/obo/GO_0050893)
Caroline-99 commented 2 weeks ago

Noticed a minor typo in the respiratory ciliated cell - will change it now

gouttegd commented 2 weeks ago

@dosumis Here’s the diff computed on the -simple artefact:

# Ontology comparison ## Left - Ontology IRI: `http://purl.obolibrary.org/obo/cl/cl-simple.owl` - Version IRI: `http://purl.obolibrary.org/obo/cl/releases/2024-11-07/cl-simple.owl` - Loaded from: `file:/Users/dpg44/Curation/Ontologies/repositories/CL/src/ontology/master/cl-simple.owl` ## Right - Ontology IRI: `http://purl.obolibrary.org/obo/cl/cl-simple.owl` - Version IRI: `http://purl.obolibrary.org/obo/cl/releases/2024-11-07/cl-simple.owl` - Loaded from: `file:/Users/dpg44/Curation/Ontologies/repositories/CL/src/ontology/pr/cl-simple.owl` ### Ontology imports ### Ontology annotations ### ciliated cell of the bronchus `http://purl.obolibrary.org/obo/CL_0002332` #### Removed - [ciliated cell of the bronchus](http://purl.obolibrary.org/obo/CL_0002332) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A ciliated cell of the bronchus." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:18757316" #### Added - [ciliated cell of the bronchus](http://purl.obolibrary.org/obo/CL_0002332) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A multi-ciliated epithelial cell located or the bronchus epithelium, characterized by a columnar shape and motile cilia on its apical surface." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:18757316" ### ciliated columnar cell of tracheobronchial tree `http://purl.obolibrary.org/obo/CL_0002145` #### Removed - [ciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) SubClassOf [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) ### lung ciliated cell `http://purl.obolibrary.org/obo/CL_1000271` #### Removed - [lung ciliated cell](http://purl.obolibrary.org/obo/CL_1000271) SubClassOf [ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0000067) ### respiratory ciliated cell `http://purl.obolibrary.org/obo/CL_4030034` #### Removed - [respiratory ciliated cell](http://purl.obolibrary.org/obo/CL_4030034) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A ciliated cell of the respiratory system. Ciliated cells are present in airway epithelium." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:21364219" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:18757316" - [respiratory ciliated cell](http://purl.obolibrary.org/obo/CL_4030034) SubClassOf [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) #### Added - [respiratory ciliated cell](http://purl.obolibrary.org/obo/CL_4030034) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A multi-ciliated epithelial cell located or the respiratory tract epithelium, characterized by a columnar shape and motile cilia on its apical surface." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:21364219" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:18757316" - [respiratory ciliated cell](http://purl.obolibrary.org/obo/CL_4030034) SubClassOf [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) - [respiratory ciliated cell](http://purl.obolibrary.org/obo/CL_4030034) SubClassOf [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368)

The -simple diff does not show any more difference on the inferred classification than the -base diff. What were you expecting to see?

For clarity, here is a terse version of the -simple diff (I’ve left aside the AnnotationAssertion axioms):

Axioms diff on -simple ``` 5 axioms in left ontology but not in right ontology: - SubClassOf( ) - SubClassOf( ) - SubClassOf( ) 4 axioms in right ontology but not in left ontology: + SubClassOf( ) + SubClassOf( ) ```

And a terse version of the -base diff:

Axioms diff on -base ``` 9 axioms in left ontology but not in right ontology: - EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - SubClassOf( ) - SubClassOf( ) - SubClassOf( ) - SubClassOf( ObjectSomeValuesFrom( )) 8 axioms in right ontology but not in left ontology: + EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + SubClassOf( ) + SubClassOf( ) ```

The -simple product does not contain any classification that is not also present in -base.

Caroline-99 commented 2 weeks ago

@dosumis - I was running the imports in a different branch, but then I switched over to review/make changes to the lung multiciliated cell PR and accidentally merged the imports into this branch. I don't think it will cause problems, but let me know if you want me to adjust anything.

dosumis commented 2 weeks ago

I think I was confused by deleted asserted axioms being inferred Before image image After image

I still think the diffs with simple are a bit easier to work with - as we have all of the asserted logical axioms but with labels in the edit file diff.

Note - I've updated one more term to follow the pattern.

Caroline-99 commented 2 weeks ago

gogoeditdiff