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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Update EC number for children of GO:0008373 sialyltransferase activity #25189

Closed pgaudet closed 1 year ago

pgaudet commented 1 year ago
pgaudet commented 1 year ago

Hi @edwong57 I made some documentation for updating EC numbers here: https://wiki.geneontology.org/Updating_EC_mappings

Let me know if the documentation has enough information to update these, or how it could be improved.

Thanks, Pascale

sjm41 commented 1 year ago

Hi @edwong57 I've run into some issues computing metabolic pathways in BioCyc because of these out-dated sialyltransferase EC xrefs. Would you be able to fix them in the GO sometime soon? Many thanks, Steven.

edwong57 commented 1 year ago

@sjm41 Apologies, I was out of town. I will take care of it this week.

edwong57 commented 1 year ago

I am also going to obsoleted GO:0004513 'neolactotetraosylceramide alpha-2,3-sialyltransferase activity' since the 2.4.99.10 Transferred entry: 2.4.99.6, itself transferred EC:2.4.3.6 and then it became a duplicate of GO:0008118 'N-acetyllactosaminide alpha-2,3-sialyltransferase activity'. They both have no annotations, but GO:0008118 has the accepted name in Expasy. Please let me know if you have any objections.

sjm41 commented 1 year ago

Thanks @edwong57 !

pgaudet commented 1 year ago

Hi @edwong57 Just FYI I- the dbxrefs should be removed from the obsoleted terms - see https://wiki.geneontology.org/Obsoleting_an_Existing_Ontology_Term#5._Cross-references (I fixed this one)

Thanks, Pascale

edwong57 commented 1 year ago

Okay. Thank you!

From: pgaudet @.> Sent: Tuesday, May 9, 2023 2:19 AM To: geneontology/go-ontology @.> Cc: Edith Wong @.>; Mention @.> Subject: Re: [geneontology/go-ontology] Update EC number for children of GO:0008373 sialyltransferase activity (Issue #25189)

Hi @edwong57https://github.com/edwong57 Just FYI I- the dbxrefs should be removed from the obsoleted terms - see https://wiki.geneontology.org/Obsoleting_an_Existing_Ontology_Term#5._Cross-references (I fixed this one)

Thanks, Pascale

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