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geneontology / go-site

A collection of metadata, tools, and files associated with the Gene Ontology public web presence.
http://geneontology.org
BSD 3-Clause "New" or "Revised" License
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Update gorule-0000037 : switched back to GO_REF:0000033 #2185

Open pgaudet opened 10 months ago

pgaudet commented 10 months ago

Old rule: IBA annotations should ONLY be assigned_by GO_Central and have PMID:21873635 as a reference

Updated to: "IBA annotations should ONLY be assigned_by GO_Central and have GO_REF:0000033 as a reference

pgaudet commented 10 months ago

PR is here: https://github.com/geneontology/go-site/pull/2186

LiNiMGI commented 9 months ago

@pgaudet during MGI import project, we found GO_REF:0000033 is listed as GOREF:0000033 in the PAINT files, please update. Thanks, Li

pgaudet commented 9 months ago

@dustine32 Can you please have a look at that one?

kltm commented 9 months ago

@pgaudet Which project does this belong to? Or is it "out" as upstream PAINT?

pgaudet commented 9 months ago

Ah I dont know if it's upstream. We dont have a PAINT project... I put it in Software essential and proactive maintenance, mostly because if the shared resources (@dustine32 )

LiNiMGI commented 9 months ago

@pgaudet @dustine32 From Lori/MGI: this problem finally also caught up with us at MGI/Production on Dec 17/18 and this affects 68984 annotations.

dustine32 commented 8 months ago

Sorry @pgaudet @LiNiMGI, didn't see this until just now! Yes, definitely a (GOREF vs. GO_REF) typo issue though it'll need to be fixed in both (1) the PAINT IBA script and (2) the GO pipeline QC test:

  1. https://github.com/pantherdb/fullgo_paint_update/blob/4b9e560aeb90c049fa9b99ff1a272ee08a2fe983/scripts/createGAF.pl#L451
  2. https://github.com/biolink/ontobio/blob/7e30b36b2c9fbe4f7638d0f2083e2ac6bd0e65c4/ontobio/io/qc.py#L530

I can generate the fixed IBA GAFs. They will then need to make it through a GO release before this fix is seen by MGI.

Also tagging @kltm