search

obophenotype / cell-ontology

An ontology of cell types
https://obophenotype.github.io/cell-ontology/
Creative Commons Attribution 4.0 International
146 stars 49 forks source link

Fixes #2673 NTR CxG type IIx muscle cell #2731

Closed aleixpuigb closed 2 weeks ago

aleixpuigb commented 3 weeks ago

Fixes #2673 NTR CxG type IIx muscle cell This PR solves problems of #2729

Caroline-99 commented 3 weeks ago

gogoeditdiff

github-actions[bot] commented 3 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 ### type IIx muscle cell `http://purl.obolibrary.org/obo/CL_4052026` #### Added - [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) [hasExactSynonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "type 2x fiber" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34727990" - [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) [hasExactSynonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "type 2x muscle fiber" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34727990" - [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "In humans, type IIx fiber contains high levels of MYLK2, enhancing contraction speed and force via myosin phosphorylation, especially under low calcium. This mechanism supports post-activation potentiation, increasing force output in fast-twitch muscles. Additionally, this fiber has abundant ACTN3 (α-actinin-3), linked to muscle power, and exhibits the highest shortening velocity among human muscle fiber types. Notably, type IIx fiber is selectively lost in aging-related sarcopenia, increases in proportion in type 2 diabetes and obesity, and is the first to degenerate in Duchenne Muscular Dystrophy, impacting muscle function across various conditions." - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34727990" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27199166" - [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) [hasExactSynonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "type 2x muscle cell" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34727990" - [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) [hasExactSynonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "type IIx muscle fiber" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1101/2024.05.15.594276" - [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) - [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) [label](http://www.w3.org/2000/01/rdf-schema#label) "type IIx muscle cell" - [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) [IAO_0000115](http://purl.obolibrary.org/obo/IAO_0000115) "A fast type II muscle cell that is part of the skeletal muscle tissue. This cell is characterized by its intermediate metabolic profile, utilizing both glycolytic and oxidative pathways for energy production. In humans, it is distinguished by the expression of myosin heavy chain 1 (MYH1)." - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1101/2024.05.15.594276" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35908794" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34727990" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36361732" - [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) [date](http://purl.org/dc/terms/date) "2024-11-04T10:26:29Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - Class: [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) - [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) SubClassOf [type II muscle cell](http://purl.obolibrary.org/obo/CL_0002212)
github-actions[bot] commented 3 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 ### type IIx muscle cell `http://purl.obolibrary.org/obo/CL_4052026` #### Added - [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "type 2x fiber" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34727990" - [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "type 2x muscle fiber" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34727990" - [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "In humans, type IIx fiber contains high levels of MYLK2, enhancing contraction speed and force via myosin phosphorylation, especially under low calcium. This mechanism supports post-activation potentiation, increasing force output in fast-twitch muscles. Additionally, this fiber has abundant ACTN3 (α-actinin-3), linked to muscle power, and exhibits the highest shortening velocity among human muscle fiber types. Notably, type IIx fiber is selectively lost in aging-related sarcopenia, increases in proportion in type 2 diabetes and obesity, and is the first to degenerate in Duchenne Muscular Dystrophy, impacting muscle function across various conditions." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34727990" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27199166" - [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "type 2x muscle cell" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34727990" - [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "type IIx muscle fiber" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1101/2024.05.15.594276" - [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) - [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) [label](http://www.w3.org/2000/01/rdf-schema#label) "type IIx muscle cell" - [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A fast type II muscle cell that is part of the skeletal muscle tissue. This cell is characterized by its intermediate metabolic profile, utilizing both glycolytic and oxidative pathways for energy production. In humans, it is distinguished by the expression of myosin heavy chain 1 (MYH1)." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35908794" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36361732" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34727990" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1101/2024.05.15.594276" - [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) [date](http://purl.org/dc/terms/date) "2024-11-04T10:26:29Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - Class: [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) - [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) SubClassOf [type II muscle cell](http://purl.obolibrary.org/obo/CL_0002212) - [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) SubClassOf [part of](http://purl.obolibrary.org/obo/BFO_0000050) some [skeletal muscle tissue](http://purl.obolibrary.org/obo/UBERON_0001134)
AvolaAmg commented 2 weeks ago

Please see in line comments!

Caroline-99 commented 2 weeks ago

gogoeditdiff