github-actions[bot] commented 1 year ago

Changes added to the edit file this PR

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# 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 ### circularized chromosome `http://purl.obolibrary.org/obo/FYPO_0002702` #### Added - [circularized chromosome](http://purl.obolibrary.org/obo/FYPO_0002702) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "NHEJ-dependent telomere fusions" - [circularized chromosome](http://purl.obolibrary.org/obo/FYPO_0002702) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "telomere end-to-end fusion" ### decreased homocitrate synthase inhibition by L-lysine `http://purl.obolibrary.org/obo/FYPO_0008054` #### Added - [decreased homocitrate synthase inhibition by L-lysine](http://purl.obolibrary.org/obo/FYPO_0008054) [creator](http://purl.org/dc/elements/1.1/creator) "vw253"^^[string](http://www.w3.org/2001/XMLSchema#string) - [decreased homocitrate synthase inhibition by L-lysine](http://purl.obolibrary.org/obo/FYPO_0008054) [label](http://www.w3.org/2000/01/rdf-schema#label) "decreased homocitrate synthase inhibition by L-lysine"@en - [decreased homocitrate synthase inhibition by L-lysine](http://purl.obolibrary.org/obo/FYPO_0008054) [date](http://purl.org/dc/elements/1.1/date) "2023-02-22T11:09:33Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [decreased homocitrate synthase inhibition by L-lysine](http://purl.obolibrary.org/obo/FYPO_0008054) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "feedback inhibition insensitive" - [decreased homocitrate synthase inhibition by L-lysine](http://purl.obolibrary.org/obo/FYPO_0008054) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A molecular function phenotype in which the observed rate of homocitrate synthase is increased, due to the absence of lysine inhibition." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20089861"^^[string](http://www.w3.org/2001/XMLSchema#string) - Class: [decreased homocitrate synthase inhibition by L-lysine](http://purl.obolibrary.org/obo/FYPO_0008054) - [decreased homocitrate synthase inhibition by L-lysine](http://purl.obolibrary.org/obo/FYPO_0008054) SubClassOf [increased catalytic activity](http://purl.obolibrary.org/obo/FYPO_0000662) ### decreased intron acceptor binding `http://purl.obolibrary.org/obo/FYPO_0008053` #### Added - [decreased intron acceptor binding](http://purl.obolibrary.org/obo/FYPO_0008053) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A molecular function phenotype in which an interaction between a protein and mRNA intron acceptor is decreased. One of the relevant gene products may be encoded by the mutated gene, or both the RNA and protein may be encoded by genes other than the mutated one." - [decreased intron acceptor binding](http://purl.obolibrary.org/obo/FYPO_0008053) [creator](http://purl.org/dc/elements/1.1/creator) "vw253"^^[string](http://www.w3.org/2001/XMLSchema#string) - [decreased intron acceptor binding](http://purl.obolibrary.org/obo/FYPO_0008053) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "'decreased 3' intron binding'" - [decreased intron acceptor binding](http://purl.obolibrary.org/obo/FYPO_0008053) [label](http://www.w3.org/2000/01/rdf-schema#label) "decreased intron acceptor binding"@en - [decreased intron acceptor binding](http://purl.obolibrary.org/obo/FYPO_0008053) [date](http://purl.org/dc/elements/1.1/date) "2023-02-22T10:59:49Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - Class: [decreased intron acceptor binding](http://purl.obolibrary.org/obo/FYPO_0008053) - [decreased intron acceptor binding](http://purl.obolibrary.org/obo/FYPO_0008053) SubClassOf [decreased protein-RNA interaction](http://purl.obolibrary.org/obo/FYPO_0002134) ### decreased ubiquitin ligase activity `http://purl.obolibrary.org/obo/FYPO_0008051` #### Added - [decreased ubiquitin ligase activity](http://purl.obolibrary.org/obo/FYPO_0008051) [creator](http://purl.org/dc/elements/1.1/creator) "vw253"^^[string](http://www.w3.org/2001/XMLSchema#string) - [decreased ubiquitin ligase activity](http://purl.obolibrary.org/obo/FYPO_0008051) [label](http://www.w3.org/2000/01/rdf-schema#label) "decreased ubiquitin ligase activity"@en - [decreased ubiquitin ligase activity](http://purl.obolibrary.org/obo/FYPO_0008051) [date](http://purl.org/dc/elements/1.1/date) "2023-02-22T10:53:57Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [decreased ubiquitin ligase activity](http://purl.obolibrary.org/obo/FYPO_0008051) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A molecular function phenotype in which the observed rate of ubiquitin ligase activity is decreased." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28572513"^^[Literal](http://www.w3.org/2000/01/rdf-schema#Literal) - Class: [decreased ubiquitin ligase activity](http://purl.obolibrary.org/obo/FYPO_0008051) - [decreased ubiquitin ligase activity](http://purl.obolibrary.org/obo/FYPO_0008051) SubClassOf [abnormal ubiquitin ligase activity](http://purl.obolibrary.org/obo/FYPO_0001912)

# Changes to ontology after reasoner runs

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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 WARN multiple_equivalent_classes polyphosphate absent from cell owl:equivalentClass blank node 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 ```

ValWood commented 1 year ago

@manulera I'm stuck here. The checks appear to have passed but review is required. I don't see how to do this.

ValWood commented 1 year ago

Also there are some errors reported above, but I don't know what they are or how to trace them. There isn't very much information.?

ValWood commented 1 year ago

...and the diff contains changes that I didn't make in this branch which seems odd?

manulera commented 1 year ago

Hi @ValWood:

You can bypass the need for a review, that's what I normally do. I don't know exactly how to do it but there is something that you can select that removes the need to ask for review.
Most of the errors are always there, I think the only "real" one is the multiple_equivalent_classes one, I can have a look.
Regarding the diff, I don't know. It does seem that you made all those changes by looking at the "raw diff" in github.

manulera commented 1 year ago

You can see the raw diff here

https://github.com/pombase/fypo/pull/4284/files

ValWood commented 1 year ago

Yes I used the raw diff, but it's hard to read...

pombase / fypo

closes #4280; closes #4279; closes #4276 closes #4270 #4284

Changes added to the edit file this PR