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geneontology / go-annotation

This repository hosts the tracker for issues pertaining to GO annotations.
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Review annotations to GO:0052665 tRNA (uracil-2'-O-)-methyltransferase activity #4745

Closed pgaudet closed 2 months ago

pgaudet commented 1 year ago

The proposal has been made to obsolete

GO:0052665 tRNA (uracil-2'-O-)-methyltransferase activity

Annotations are here: https://docs.google.com/spreadsheets/d/1Oh1E8Xa36Gj6ZYltz9SBebiO2CF6-zFBeaY8ox2UmZU/edit#gid=0

deustp01 commented 1 year ago

We use this one. Is there a suggested replacement term? (Or is that provided later in the obsoletion / review process as now organized?)

pgaudet commented 1 year ago

Reactome describes a reaction methylating U44 ( EC:2.1.1.211 / RHEA:43100), which is not yet in GO.

suzialeksander commented 3 months ago

Still 2 Ecocyc remain

amandamackie commented 3 months ago

I've removed the term in EcoCyc however we do require a term for EC 2.1.1.200 -- tRNA (cytidine32/uridine32-2′-O)-methyltransferase. Noting that there remains a specific term for methylation at the C32 position (GO:0106339).

Amanda

pgaudet commented 3 months ago

Thanks!

pgaudet commented 3 months ago

@amandamackie - can you use GO:0106339 which corresponds to EC 2.1.1.200?

I am not sure I understand your comment,

Thanks, Pascale

amandamackie commented 3 months ago

The definition for GO:0106339 looks to be specific for tRNA cytidine 32 methylation but I require a term for tRNA uridine 32 methylation. I can use the parent term GO:0016300 tRNA (uridine) methyltransferase activity

pgaudet commented 3 months ago

Thanks for clarifying @amandamackie !

This is quite odd. I opened an ontology ticket to address this: https://github.com/geneontology/go-ontology/issues/28550 Basically I think we should align with EC and add the two possible substrates back in this reaction.

Let's wait for @sjm41 ti be back from vacation to complete this.

Thanks, Pascale

suzialeksander commented 2 months ago

Noting the term in this ticket has been obsoleted GO:0052665 obsolete tRNA (uracil-2'-O-)-methyltransferase activity

pgaudet commented 2 months ago

@deustp01 Have you moved the Reactome annotation (Reactome:R-HSA-6788707 > GO:tRNA (uracil-2'-O-)-methyltransferase activity ; GO:0052665) to new term GO:0141101 tRNA(Ser) (uridine(44)-2'-O-)-methyltransferase activity? If so, then we can close this.

deustp01 commented 2 months ago

Have you moved the Reactome annotation?

Yes, all done. Sorry, I forgot to note the edit to the GitHub ticket.