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pombase / fypo

Fission Yeast Phenotype Ontology
Creative Commons Attribution 4.0 International
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“closes #4392

Closed ValWood closed 1 year ago

github-actions[bot] commented 1 year ago

Hi @ValWood! It seems you forgot to run normalised_xsd_string on your PR. Please run it and commit the changes.

github-actions[bot] commented 1 year 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 U6 snRNP assembly `http://purl.obolibrary.org/obo/FYPO_0008112` #### Added - [abnormal U6 snRNP assembly](http://purl.obolibrary.org/obo/FYPO_0008112) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw"^^[string](http://www.w3.org/2001/XMLSchema#string) - [abnormal U6 snRNP assembly](http://purl.obolibrary.org/obo/FYPO_0008112) [creation_dat](http://www.geneontology.org/formats/oboInOwl#creation_dat) "2023-07-11T12:31:29Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [abnormal U6 snRNP assembly](http://purl.obolibrary.org/obo/FYPO_0008112) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which any process of U6 snRNP complex assembly is abnormal." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37403782" - [abnormal U6 snRNP assembly](http://purl.obolibrary.org/obo/FYPO_0008112) [label](http://www.w3.org/2000/01/rdf-schema#label) "abnormal U6 snRNP assembly"@en - Class: [abnormal U6 snRNP assembly](http://purl.obolibrary.org/obo/FYPO_0008112) - [abnormal U6 snRNP assembly](http://purl.obolibrary.org/obo/FYPO_0008112) SubClassOf [abnormal ribonucleoprotein complex assembly](http://purl.obolibrary.org/obo/FYPO_0003628) ### abnormal snRNA modification `http://purl.obolibrary.org/obo/FYPO_0008111` #### Added - [abnormal snRNA modification](http://purl.obolibrary.org/obo/FYPO_0008111) [creation_dat](http://www.geneontology.org/formats/oboInOwl#creation_dat) "2023-07-11T12:26:19Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [abnormal snRNA modification](http://purl.obolibrary.org/obo/FYPO_0008111) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which snRNA modification is abnormal. All snRNA modification may be abnormal, or one or more specific snRNA modifications may be selectively affected." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37403782" - [abnormal snRNA modification](http://purl.obolibrary.org/obo/FYPO_0008111) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw"^^[string](http://www.w3.org/2001/XMLSchema#string) - [abnormal snRNA modification](http://purl.obolibrary.org/obo/FYPO_0008111) [label](http://www.w3.org/2000/01/rdf-schema#label) "abnormal snRNA modification"@en - Class: [abnormal snRNA modification](http://purl.obolibrary.org/obo/FYPO_0008111) - [abnormal snRNA modification](http://purl.obolibrary.org/obo/FYPO_0008111) SubClassOf [abnormal RNA modification](http://purl.obolibrary.org/obo/FYPO_0000370) ### abnormal transporter activity `http://purl.obolibrary.org/obo/FYPO_0002116` #### Removed - [abnormal transporter activity](http://purl.obolibrary.org/obo/FYPO_0002116) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A molecular function phenotype in which the observed rate of a specified transporter activity is abnormal." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:mah" - [abnormal transporter activity](http://purl.obolibrary.org/obo/FYPO_0002116) [label](http://www.w3.org/2000/01/rdf-schema#label) "abnormal transporter activity" - [abnormal transporter activity](http://purl.obolibrary.org/obo/FYPO_0002116) EquivalentTo [has part](http://purl.obolibrary.org/obo/BFO_0000051) some ([quality](http://purl.obolibrary.org/obo/PATO_0000001) and ([characteristic of](http://purl.obolibrary.org/obo/RO_0000052) some [transporter activity](http://purl.obolibrary.org/obo/GO_0005215)) and ([has modifier](http://purl.obolibrary.org/obo/RO_0002573) some [abnormal](http://purl.obolibrary.org/obo/PATO_0000460))) #### Added - [abnormal transporter activity](http://purl.obolibrary.org/obo/FYPO_0002116) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A molecular function phenotype in which the observed rate of a specified transmembrane transporter activity is abnormal." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:mah" - [abnormal transporter activity](http://purl.obolibrary.org/obo/FYPO_0002116) [label](http://www.w3.org/2000/01/rdf-schema#label) "abnormal transmembrane transporter activity" - [abnormal transporter activity](http://purl.obolibrary.org/obo/FYPO_0002116) EquivalentTo [has part](http://purl.obolibrary.org/obo/BFO_0000051) some ([quality](http://purl.obolibrary.org/obo/BFO_0000019) and ([characteristic of](http://purl.obolibrary.org/obo/RO_0000052) some [transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0022857)) and ([has modifier](http://purl.obolibrary.org/obo/RO_0002573) some [abnormal](http://purl.obolibrary.org/obo/PATO_0000460))) ### abolished U6 2'-O-snRNA methylation `http://purl.obolibrary.org/obo/FYPO_0003621` #### Added - [abolished U6 2'-O-snRNA methylation](http://purl.obolibrary.org/obo/FYPO_0003621) SubClassOf [abnormal snRNA modification](http://purl.obolibrary.org/obo/FYPO_0008111) ### abolished U6 2'-O-snRNA methylation at residue A64 `http://purl.obolibrary.org/obo/FYPO_0008109` #### Added - [abolished U6 2'-O-snRNA methylation at residue A64](http://purl.obolibrary.org/obo/FYPO_0008109) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which posttranscriptional addition of a methyl group to the 2'-oxygen atom of the adenine residue at position 64 in an U6 snRNA molecule is abolished." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37403782" - [abolished U6 2'-O-snRNA methylation at residue A64](http://purl.obolibrary.org/obo/FYPO_0008109) [label](http://www.w3.org/2000/01/rdf-schema#label) "abolished U6 2'-O-snRNA methylation at residue A64"@en - [abolished U6 2'-O-snRNA methylation at residue A64](http://purl.obolibrary.org/obo/FYPO_0008109) [creation_dat](http://www.geneontology.org/formats/oboInOwl#creation_dat) "2023-07-11T12:16:24Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [abolished U6 2'-O-snRNA methylation at residue A64](http://purl.obolibrary.org/obo/FYPO_0008109) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw"^^[string](http://www.w3.org/2001/XMLSchema#string) - Class: [abolished U6 2'-O-snRNA methylation at residue A64](http://purl.obolibrary.org/obo/FYPO_0008109) - [abolished U6 2'-O-snRNA methylation at residue A64](http://purl.obolibrary.org/obo/FYPO_0008109) SubClassOf [abolished U6 2'-O-snRNA methylation](http://purl.obolibrary.org/obo/FYPO_0003621) ### decreased U6 2'-O-snRNA methylation at residue A64 `http://purl.obolibrary.org/obo/FYPO_0008110` #### Added - [decreased U6 2'-O-snRNA methylation at residue A64](http://purl.obolibrary.org/obo/FYPO_0008110) [label](http://www.w3.org/2000/01/rdf-schema#label) "decreased U6 2'-O-snRNA methylation at residue A64"@en - [decreased U6 2'-O-snRNA methylation at residue A64](http://purl.obolibrary.org/obo/FYPO_0008110) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw"^^[string](http://www.w3.org/2001/XMLSchema#string) - [decreased U6 2'-O-snRNA methylation at residue A64](http://purl.obolibrary.org/obo/FYPO_0008110) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which posttranscriptional addition of a methyl group to the 2'-oxygen atom of the adenine residue at position 64 in an U6 snRNA molecule is decreased." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37403782" - [decreased U6 2'-O-snRNA methylation at residue A64](http://purl.obolibrary.org/obo/FYPO_0008110) [creation_dat](http://www.geneontology.org/formats/oboInOwl#creation_dat) "2023-07-11T12:20:26Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - Class: [decreased U6 2'-O-snRNA methylation at residue A64](http://purl.obolibrary.org/obo/FYPO_0008110) - [decreased U6 2'-O-snRNA methylation at residue A64](http://purl.obolibrary.org/obo/FYPO_0008110) SubClassOf [decreased RNA modification](http://purl.obolibrary.org/obo/FYPO_0000372) - [decreased U6 2'-O-snRNA methylation at residue A64](http://purl.obolibrary.org/obo/FYPO_0008110) SubClassOf [abnormal snRNA modification](http://purl.obolibrary.org/obo/FYPO_0008111) ### decreased phosphoglycerate mutase activity `http://purl.obolibrary.org/obo/FYPO_0008116` #### Added - [decreased phosphoglycerate mutase activity](http://purl.obolibrary.org/obo/FYPO_0008116) [creation_dat](http://www.geneontology.org/formats/oboInOwl#creation_dat) "2023-07-11T13:25:54Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [decreased phosphoglycerate mutase activity](http://purl.obolibrary.org/obo/FYPO_0008116) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw"^^[string](http://www.w3.org/2001/XMLSchema#string) - [decreased phosphoglycerate mutase activity](http://purl.obolibrary.org/obo/FYPO_0008116) [label](http://www.w3.org/2000/01/rdf-schema#label) "decreased phosphoglycerate mutase activity"@en - [decreased phosphoglycerate mutase activity](http://purl.obolibrary.org/obo/FYPO_0008116) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A molecular function phenotype in which the observed rate of a phosphoglycerate mutase activity is decreased." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:11106417" - Class: [decreased phosphoglycerate mutase activity](http://purl.obolibrary.org/obo/FYPO_0008116) - [decreased phosphoglycerate mutase activity](http://purl.obolibrary.org/obo/FYPO_0008116) EquivalentTo [has part](http://purl.obolibrary.org/obo/BFO_0000051) some ([decreased rate](http://purl.obolibrary.org/obo/PATO_0000911) and ([characteristic of](http://purl.obolibrary.org/obo/RO_0000052) some [phosphoglycerate mutase activity](http://purl.obolibrary.org/obo/GO_0004619))) - [decreased phosphoglycerate mutase activity](http://purl.obolibrary.org/obo/FYPO_0008116) SubClassOf [decreased catalytic activity](http://purl.obolibrary.org/obo/FYPO_0000663) ### increased cell population growth on sorbitol carbon source `http://purl.obolibrary.org/obo/FYPO_0008115` #### Added - [increased cell population growth on sorbitol carbon source](http://purl.obolibrary.org/obo/FYPO_0008115) [creation_dat](http://www.geneontology.org/formats/oboInOwl#creation_dat) "2023-07-11T13:07:58Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [increased cell population growth on sorbitol carbon source](http://purl.obolibrary.org/obo/FYPO_0008115) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "fission_yeast_phenotype" - [increased cell population growth on sorbitol carbon source](http://purl.obolibrary.org/obo/FYPO_0008115) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Note that cell growth terms refer to growth under aerobic conditions unless stated otherwise." - [increased cell population growth on sorbitol carbon source](http://purl.obolibrary.org/obo/FYPO_0008115) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A vegetative cell population growth phenotype in which cell growth is increased relative to normal in a medium containing sorbitol as the carbon source." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:15537393" - [increased cell population growth on sorbitol carbon source](http://purl.obolibrary.org/obo/FYPO_0008115) [label](http://www.w3.org/2000/01/rdf-schema#label) "increased cell population growth on sorbitol carbon source"@en - [increased cell population growth on sorbitol carbon source](http://purl.obolibrary.org/obo/FYPO_0008115) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw"^^[string](http://www.w3.org/2001/XMLSchema#string) - Class: [increased cell population growth on sorbitol carbon source](http://purl.obolibrary.org/obo/FYPO_0008115) - [increased cell population growth on sorbitol carbon source](http://purl.obolibrary.org/obo/FYPO_0008115) SubClassOf [increased vegetative cell population growth](http://purl.obolibrary.org/obo/FYPO_0004557) ### increased intron retention `http://purl.obolibrary.org/obo/FYPO_0008113` #### Added - [increased intron retention](http://purl.obolibrary.org/obo/FYPO_0008113) [creation_dat](http://www.geneontology.org/formats/oboInOwl#creation_dat) "2023-07-11T12:34:21Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [increased intron retention](http://purl.obolibrary.org/obo/FYPO_0008113) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw"^^[string](http://www.w3.org/2001/XMLSchema#string) - [increased intron retention](http://purl.obolibrary.org/obo/FYPO_0008113) [label](http://www.w3.org/2000/01/rdf-schema#label) "increased intron retention"@en - [increased intron retention](http://purl.obolibrary.org/obo/FYPO_0008113) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which introns are retained at some, but not all introns at a higher level with increased frequency. Weak donor sequences are more affected." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37403782" - Class: [increased intron retention](http://purl.obolibrary.org/obo/FYPO_0008113) - [increased intron retention](http://purl.obolibrary.org/obo/FYPO_0008113) SubClassOf [intron-specific abnormal mRNA splicing, via spliceosome](http://purl.obolibrary.org/obo/FYPO_0003244) ### normal transporter activity `http://purl.obolibrary.org/obo/FYPO_0002115` #### Removed - [normal transporter activity](http://purl.obolibrary.org/obo/FYPO_0002115) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A molecular function phenotype in which the observed rate of a specified transporter activity is normal (i.e. indistinguishable from wild type)." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:mah" - [normal transporter activity](http://purl.obolibrary.org/obo/FYPO_0002115) [label](http://www.w3.org/2000/01/rdf-schema#label) "normal transporter activity" - [normal transporter activity](http://purl.obolibrary.org/obo/FYPO_0002115) EquivalentTo [has part](http://purl.obolibrary.org/obo/BFO_0000051) some ([quality](http://purl.obolibrary.org/obo/PATO_0000001) and ([characteristic of](http://purl.obolibrary.org/obo/RO_0000052) some [transporter activity](http://purl.obolibrary.org/obo/GO_0005215)) and ([has modifier](http://purl.obolibrary.org/obo/RO_0002573) some [normal](http://purl.obolibrary.org/obo/PATO_0000461))) #### Added - [normal transporter activity](http://purl.obolibrary.org/obo/FYPO_0002115) [label](http://www.w3.org/2000/01/rdf-schema#label) "normal transmembrane transporter activity" - [normal transporter activity](http://purl.obolibrary.org/obo/FYPO_0002115) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A molecular function phenotype in which the observed rate of a specified transmembrane transporter activity is normal (i.e. indistinguishable from wild type)." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:mah" - [normal transporter activity](http://purl.obolibrary.org/obo/FYPO_0002115) EquivalentTo [has part](http://purl.obolibrary.org/obo/BFO_0000051) some ([quality](http://purl.obolibrary.org/obo/BFO_0000019) and ([characteristic of](http://purl.obolibrary.org/obo/RO_0000052) some [transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0022857)) and ([has modifier](http://purl.obolibrary.org/obo/RO_0002573) some [normal](http://purl.obolibrary.org/obo/PATO_0000461))) ### sensitive to amiloride `http://purl.obolibrary.org/obo/FYPO_0008114` #### Added - [sensitive to amiloride](http://purl.obolibrary.org/obo/FYPO_0008114) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw"^^[string](http://www.w3.org/2001/XMLSchema#string) - [sensitive to amiloride](http://purl.obolibrary.org/obo/FYPO_0008114) [label](http://www.w3.org/2000/01/rdf-schema#label) "sensitive to amiloride"@en - [sensitive to amiloride](http://purl.obolibrary.org/obo/FYPO_0008114) [creation_dat](http://www.geneontology.org/formats/oboInOwl#creation_dat) "2023-07-11T12:43:36Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [sensitive to amiloride](http://purl.obolibrary.org/obo/FYPO_0008114) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A phenotype observed in the vegetative growth phase of the life cycle in which cells show increased sensitivity to amiloride. Cells stop growing (and may die) at a concentration of amiloride that allows wild type cells to grow." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:15537393" - Class: [sensitive to amiloride](http://purl.obolibrary.org/obo/FYPO_0008114) - [sensitive to amiloride](http://purl.obolibrary.org/obo/FYPO_0008114) SubClassOf [increased sensitivity to chemical during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0000127) ### snoRNA guided rRNA 2'-O-methylation abolished at specific site `http://purl.obolibrary.org/obo/FYPO_0003720` #### Removed - [snoRNA guided rRNA 2'-O-methylation abolished at specific site](http://purl.obolibrary.org/obo/FYPO_0003720) SubClassOf [abnormal RNA modification](http://purl.obolibrary.org/obo/FYPO_0000370) #### Added - [snoRNA guided rRNA 2'-O-methylation abolished at specific site](http://purl.obolibrary.org/obo/FYPO_0003720) SubClassOf [abnormal snRNA modification](http://purl.obolibrary.org/obo/FYPO_0008111) ### snoRNA guided rRNA pseudouridine synthesis abolished at specific site `http://purl.obolibrary.org/obo/FYPO_0003699` #### Removed - [snoRNA guided rRNA pseudouridine synthesis abolished at specific site](http://purl.obolibrary.org/obo/FYPO_0003699) SubClassOf [abnormal RNA modification](http://purl.obolibrary.org/obo/FYPO_0000370) #### Added - [snoRNA guided rRNA pseudouridine synthesis abolished at specific site](http://purl.obolibrary.org/obo/FYPO_0003699) SubClassOf [abnormal snRNA modification](http://purl.obolibrary.org/obo/FYPO_0008111) ### transporter activity phenotype `http://purl.obolibrary.org/obo/FYPO_0002114` #### Removed - [transporter activity phenotype](http://purl.obolibrary.org/obo/FYPO_0002114) [label](http://www.w3.org/2000/01/rdf-schema#label) "transporter activity phenotype" - [transporter activity phenotype](http://purl.obolibrary.org/obo/FYPO_0002114) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A phenotype that affects a transporter activity." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:mah" - [transporter activity phenotype](http://purl.obolibrary.org/obo/FYPO_0002114) EquivalentTo [has part](http://purl.obolibrary.org/obo/BFO_0000051) some ([phenotype](http://purl.obolibrary.org/obo/FYPO_0000001) and ([characteristic of](http://purl.obolibrary.org/obo/RO_0000052) some [transporter activity](http://purl.obolibrary.org/obo/GO_0005215))) #### Added - [transporter activity phenotype](http://purl.obolibrary.org/obo/FYPO_0002114) [label](http://www.w3.org/2000/01/rdf-schema#label) "transmembrane transporter activity phenotype" - [transporter activity phenotype](http://purl.obolibrary.org/obo/FYPO_0002114) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A phenotype that affects a transmembrane transporter activity." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:mah" - [transporter activity phenotype](http://purl.obolibrary.org/obo/FYPO_0002114) EquivalentTo [has part](http://purl.obolibrary.org/obo/BFO_0000051) some ([phenotype](http://purl.obolibrary.org/obo/FYPO_0000001) and ([characteristic of](http://purl.obolibrary.org/obo/RO_0000052) some [transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0022857)))
# 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 ```
github-actions[bot] commented 1 year ago

Hi @ValWood! It seems you forgot to run normalised_xsd_string on your PR. Please run it and commit the changes.