pombase / fypo

Fission Yeast Phenotype Ontology
Creative Commons Attribution 4.0 International
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‘#4415 #4417

Closed ValWood closed 10 months ago

github-actions[bot] commented 10 months ago

Changes added to the edit file this PR

Click to expand # Ontology comparison ## Left - Ontology IRI: `http://purl.obolibrary.org/obo/fypo.owl` - Version IRI: *None* - Loaded from: `file:/__w/fypo/fypo/master/src/ontology/fypo-edit.owl` ## Right - Ontology IRI: `http://purl.obolibrary.org/obo/fypo.owl` - Version IRI: *None* - Loaded from: `file:/__w/fypo/fypo/src/ontology/fypo-edit.owl` ### Ontology imports ### Ontology annotations ### abnormal mitochondrial fusion `http://purl.obolibrary.org/obo/FYPO_0008089` #### Added - [abnormal mitochondrial fusion](http://purl.obolibrary.org/obo/FYPO_0008089) [label](http://www.w3.org/2000/01/rdf-schema#label) "abnormal mitochondrial fusion"@en - [abnormal mitochondrial fusion](http://purl.obolibrary.org/obo/FYPO_0008089) [creation_dat](http://www.geneontology.org/formats/oboInOwl#creation_dat) "2023-08-31T16:44:05Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [abnormal mitochondrial fusion](http://purl.obolibrary.org/obo/FYPO_0008089) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype in which mitochondrion fusion is abnormal." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37590302" - [abnormal mitochondrial fusion](http://purl.obolibrary.org/obo/FYPO_0008089) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - Class: [abnormal mitochondrial fusion](http://purl.obolibrary.org/obo/FYPO_0008089) - [abnormal mitochondrial fusion](http://purl.obolibrary.org/obo/FYPO_0008089) EquivalentTo [has_part](http://purl.obolibrary.org/obo/BFO_0000051) some ([quality](http://purl.obolibrary.org/obo/PATO_0000001) and ([inheres in part of](http://purl.obolibrary.org/obo/RO_0002314) some [mitochondrial fusion](http://purl.obolibrary.org/obo/GO_0008053)) and ([qualifier](http://purl.obolibrary.org/obo/RO_0002573) some [abnormal](http://purl.obolibrary.org/obo/PATO_0000460))) - [abnormal mitochondrial fusion](http://purl.obolibrary.org/obo/FYPO_0008089) SubClassOf [abnormal cellular process](http://purl.obolibrary.org/obo/FYPO_0000628) ### altered tRNA level during vegetative growth `http://purl.obolibrary.org/obo/FYPO_0008101` #### Added - [altered tRNA level during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008101) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell phenotype in which the amount of tRNA measured in a cell differs from normal when the cell is in the vegetative growth phase of the life cycle." - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PMID:36794724" - [altered tRNA level during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008101) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [altered tRNA level during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008101) [label](http://www.w3.org/2000/01/rdf-schema#label) "altered tRNA level during vegetative growth"@en - [altered tRNA level during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008101) [creation_dat](http://www.geneontology.org/formats/oboInOwl#creation_dat) "2023-08-31T16:56:39Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [altered tRNA level during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008101) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Consider annotating to a term describing abnormal transcription or abnormal regulation of transcription, but note that changes in RNA levels may result from changes in RNA stability as well as changes in transcription. We recommend noting which RNA(s) were used in the assay when annotating to this term." - Class: [altered tRNA level during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008101) - [altered tRNA level during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008101) SubClassOf [altered RNA level during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0001326) ### increased mature tRNA level during vegetative growth `http://purl.obolibrary.org/obo/FYPO_0002564` #### Added - [increased mature tRNA level during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0002564) SubClassOf [altered tRNA level during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008101) ### increased polyadenylated 25S rRNA level `http://purl.obolibrary.org/obo/FYPO_0004678` #### Removed - [increased polyadenylated 25S rRNA level](http://purl.obolibrary.org/obo/FYPO_0004678) SubClassOf [increased RNA level during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0000825) - [increased polyadenylated 25S rRNA level](http://purl.obolibrary.org/obo/FYPO_0004678) SubClassOf [altered rRNA or precursor level](http://purl.obolibrary.org/obo/FYPO_0005996) #### Added - [increased polyadenylated 25S rRNA level](http://purl.obolibrary.org/obo/FYPO_0004678) SubClassOf [increased polyadenylated rRNA level](http://purl.obolibrary.org/obo/FYPO_0008091) ### increased polyadenylated 5S rRNA level during cellular response to phosphate starvation `http://purl.obolibrary.org/obo/FYPO_0008100` #### Added - [increased polyadenylated 5S rRNA level during cellular response to phosphate starvation](http://purl.obolibrary.org/obo/FYPO_0008100) [creation_dat](http://www.geneontology.org/formats/oboInOwl#creation_dat) "2023-08-31T16:52:27Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [increased polyadenylated 5S rRNA level during cellular response to phosphate starvation](http://purl.obolibrary.org/obo/FYPO_0008100) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Consider annotating to a term describing abnormal transcription or abnormal regulation of transcription, but note that changes in RNA levels may result from changes in RNA stability as well as changes in transcription. We recommend noting which RNA(s) were used in the assay when annotating to this term." - [increased polyadenylated 5S rRNA level during cellular response to phosphate starvation](http://purl.obolibrary.org/obo/FYPO_0008100) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [increased polyadenylated 5S rRNA level during cellular response to phosphate starvation](http://purl.obolibrary.org/obo/FYPO_0008100) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of mature, polyadenylated 5S rRNA measured in a cell is higher than normal during phosphate starvation." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36794724" - [increased polyadenylated 5S rRNA level during cellular response to phosphate starvation](http://purl.obolibrary.org/obo/FYPO_0008100) [label](http://www.w3.org/2000/01/rdf-schema#label) "increased polyadenylated 5S rRNA level during cellular response to phosphate starvation"@en - Class: [increased polyadenylated 5S rRNA level during cellular response to phosphate starvation](http://purl.obolibrary.org/obo/FYPO_0008100) - [increased polyadenylated 5S rRNA level during cellular response to phosphate starvation](http://purl.obolibrary.org/obo/FYPO_0008100) SubClassOf [increased polyadenylated rRNA level](http://purl.obolibrary.org/obo/FYPO_0008091) ### increased polyadenylated rRNA level `http://purl.obolibrary.org/obo/FYPO_0008091` #### Added - [increased polyadenylated rRNA level](http://purl.obolibrary.org/obo/FYPO_0008091) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of mature, polyadenylated rRNA measured in a cell is higher than normal." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36794724" - [increased polyadenylated rRNA level](http://purl.obolibrary.org/obo/FYPO_0008091) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Consider annotating to a term describing abnormal transcription or abnormal regulation of transcription, but note that changes in RNA levels may result from changes in RNA stability as well as changes in transcription. We recommend noting which RNA(s) were used in the assay when annotating to this term." - [increased polyadenylated rRNA level](http://purl.obolibrary.org/obo/FYPO_0008091) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [increased polyadenylated rRNA level](http://purl.obolibrary.org/obo/FYPO_0008091) [label](http://www.w3.org/2000/01/rdf-schema#label) "increased polyadenylated rRNA level"@en - [increased polyadenylated rRNA level](http://purl.obolibrary.org/obo/FYPO_0008091) [creation_dat](http://www.geneontology.org/formats/oboInOwl#creation_dat) "2023-08-31T16:49:14Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - Class: [increased polyadenylated rRNA level](http://purl.obolibrary.org/obo/FYPO_0008091) - [increased polyadenylated rRNA level](http://purl.obolibrary.org/obo/FYPO_0008091) SubClassOf [increased RNA level during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0000825) - [increased polyadenylated rRNA level](http://purl.obolibrary.org/obo/FYPO_0008091) SubClassOf [altered rRNA or precursor level](http://purl.obolibrary.org/obo/FYPO_0005996) ### increased pre-tRNA level during vegetative growth `http://purl.obolibrary.org/obo/FYPO_0006749` #### Added - [increased pre-tRNA level during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0006749) SubClassOf [altered tRNA level during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008101) ### increased tRNA level during cellular response to phosphate starvation `http://purl.obolibrary.org/obo/FYPO_0008102` #### Added - [increased tRNA level during cellular response to phosphate starvation](http://purl.obolibrary.org/obo/FYPO_0008102) [label](http://www.w3.org/2000/01/rdf-schema#label) "increased tRNA level during cellular response to phosphate starvation"@en - [increased tRNA level during cellular response to phosphate starvation](http://purl.obolibrary.org/obo/FYPO_0008102) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell phenotype in which the amount of tRNA measured in a cell is increased from normal when the cell is in the vegetative growth phase of the life cycle during phosphate starvation." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36794724" - [increased tRNA level during cellular response to phosphate starvation](http://purl.obolibrary.org/obo/FYPO_0008102) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Consider annotating to a term describing abnormal transcription or abnormal regulation of transcription, but note that changes in RNA levels may result from changes in RNA stability as well as changes in transcription. We recommend noting which RNA(s) were used in the assay when annotating to this term." - [increased tRNA level during cellular response to phosphate starvation](http://purl.obolibrary.org/obo/FYPO_0008102) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [increased tRNA level during cellular response to phosphate starvation](http://purl.obolibrary.org/obo/FYPO_0008102) [creation_dat](http://www.geneontology.org/formats/oboInOwl#creation_dat) "2023-08-31T17:04:56Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - Class: [increased tRNA level during cellular response to phosphate starvation](http://purl.obolibrary.org/obo/FYPO_0008102) - [increased tRNA level during cellular response to phosphate starvation](http://purl.obolibrary.org/obo/FYPO_0008102) SubClassOf [altered tRNA level during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008101) ### normal mitochondrial inheritance `http://purl.obolibrary.org/obo/FYPO_0008108` #### Added - [normal mitochondrial inheritance](http://purl.obolibrary.org/obo/FYPO_0008108) [label](http://www.w3.org/2000/01/rdf-schema#label) "normal mitochondrial inheritance"@en - [normal mitochondrial inheritance](http://purl.obolibrary.org/obo/FYPO_0008108) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [normal mitochondrial inheritance](http://purl.obolibrary.org/obo/FYPO_0008108) [creation_dat](http://www.geneontology.org/formats/oboInOwl#creation_dat) "2023-08-31T17:12:24Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [normal mitochondrial inheritance](http://purl.obolibrary.org/obo/FYPO_0008108) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A phenotype in which mitochondrial is normal (i.e. indistinguishable from wild type)." - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PMID:15710398" - Class: [normal mitochondrial inheritance](http://purl.obolibrary.org/obo/FYPO_0008108) - [normal mitochondrial inheritance](http://purl.obolibrary.org/obo/FYPO_0008108) EquivalentTo [has_part](http://purl.obolibrary.org/obo/BFO_0000051) some ([quality](http://purl.obolibrary.org/obo/PATO_0000001) and ([inheres_in](http://purl.obolibrary.org/obo/RO_0000052) some [mitochondrion inheritance](http://purl.obolibrary.org/obo/GO_0000001)) and ([qualifier](http://purl.obolibrary.org/obo/RO_0002573) some [normal](http://purl.obolibrary.org/obo/PATO_0000461))) - [normal mitochondrial inheritance](http://purl.obolibrary.org/obo/FYPO_0008108) SubClassOf [normal cellular process](http://purl.obolibrary.org/obo/FYPO_0000627)
# Changes to ontology after reasoner runs
Click to expand Coming soon >
# Errors reported ``` Level Rule Name Subject Property Value WARN missing_definition output_of definition WARN missing_definition preceded_by definition WARN missing_definition precedes definition INFO lowercase_definition has_output definition p has output c if either: p has direct output c or p has output input c. Implies that if p happens, c always ensues. INFO missing_superclass phenotype rdfs:subClassOf INFO missing_superclass normal inositol heptakisphosphate 5-kinase activity rdfs:subClassOf ```