pgaudet

GO:0044272 sulfur compound biosynthetic process

Clean up datasets/goa.yaml

1

https://github.com/geneontology/go-site/blob/master/metadata/datasets/goa.yaml Removed all isoform, RNA, complexes GPIs and GPADs for human, chicken, dog, pig and cow. PR is here: https://github.com/geneontology/go-site/pull/2455 @kltm Do you need to update something in the pipeline...

Update goa.yaml to remove and add bacterial and viral species

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We noticed that the list requested in https://github.com/geneontology/neo/issues/116 included organisms without a reference proteome, so we were attempting to load >1.5M entries. New list: https://docs.google.com/spreadsheets/d/1dQ0gN2HQjq2IFuXQrUdE5uRmMvZaUuylYQ1RvclrCqc/edit?gid=1998866383#gid=1998866383 Citrobacter koseri (Citrobacter diversus) |...

GORULE reports - Small formatting issue

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Hi @mugitty In individual report pages, for example https://release.geneontology.org/2024-11-03/reports/assigned-by-dictybase-report.html the 'quotes' resolve as ASCI codes If this is an easy fix, can it be made prettier? Thanks, Pascale

- gorule-0000009 Annotation Intersection Alerts - gorule-0000036 Report annotations that involve gene products where the gene product is annotated to a term 'x' and 'regulation of X' (multiple annotations involved)...

Dear all, The proposal has been made to obsolete: - GO:0018258 protein O-linked glycosylation via hydroxyproline - GO:0018242 protein O-linked glycosylation via serine - GO:0018243 protein O-linked glycosylation via threonine...

Obsoletion request: GO:0102306 | benzil reductase [(S)-benzoin-forming] activity

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GO:0102306 | benzil reductase [(S)-benzoin-forming] activity The reason for obsoletion is that this is not a physiologically relevant substrate. @edwong57 please add the RHEA cross reference to the parent term...

Guidelines for cross-reference types

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Splitting this discussion from https://github.com/geneontology/go-ontology/issues/28558#issuecomment-2527291242 We want to have guidelines for cross-reference types, in particular narrow versus related. We have some guidelines here: https://wiki.geneontology.org/Guidelines_for_database_cross_references#Exact,_broad,_narrow_general_database_cross_references but they could be more precise....

Please provide as much information as you can: * **GO term ID and Label** GO:0006561 proline biosynthetic process * **Reason for deprecation** The term represents the same pathway as GO:0055129...

GO:0034508 : revise term name to: centromeric chromatin formation

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Hi, We had discussed some time ago to change the label of GO:0034508 centromere complex assembly to centromeric chromatin formation. This would imply moving the terms under chromatin remodeling; probably...