Review annotations to protein dimerization activity (GO:0046983)

[vanaukenk]

To continue the work on revising annotations made to GO terms that reflect stoichiometry of interactions, we would like curators to review a subset of manual annotations to 'protein dimerization activity' (GO:0046983).

A few things for curators to note:

1. In the spreadsheet, I've listed all existing annotations, but only those with a colored background need to be manually reviewed. The other annotations should be able to be changed en masse programmatically (depending on how groups handle the bulk changes).

2. As the suggested changes to existing annotations depends on the evidence code used, I'm going to put annotations for each evidence code in a separate comment to hopefully make it easier for curators to hone in on the ones they need to review.

Any questions, please add a comment to the ticket. Thx.

https://docs.google.com/spreadsheets/d/1ymWzjGnFhkJ9oZTX-bX_nENkKmASQW1dM3eISOa72dg

[vanaukenk]

IDA

Annotations to GO:00046983 (protein dimerization activity) and evidence code ECO:0000314 (IDA) Issue: no entry in the With/From field Need manual review to see if they can be changed (see spreadsheet) How many of these and who? AgBase - 2 @jinhuiz ~ARUK-UCL - 1~ ~BHF-UCL - 2~ CAFA - 1 ~dictyBase - 2~ ~FlyBase - 2~ GeneDB - 8 @uliboehme ~MGI - 7 (fixed)~ ~RGD - 11 (fixed)~ UniProt - 41 ZFIN - 3

[vanaukenk]

NAS

Annotations to GO:00046983 (protein dimerization activity) and evidence code ECO:0000303 (NAS) Issue: no entry in the With/From field Need manual review to see if they can be changed to an experimental code If not, delete the annotation How many of these and who? AgBase - 1 ~FlyBase - 1~ UniProt - 6

[vanaukenk]

IMP

Annotation to Annotations to GO:00046983 (protein dimerization activity) and evidence code ECO:0000315 (IMP) Issue: no entry in the With/From field Need manual review to see if they can be changed to IPI (if not already there) AgBase - 1 ~MGI - 2 cannot find these~ ~RGD -2 (fixed)~

[vanaukenk]

RCA

Annotations to GO:00046983 (protein dimerization activity) and evidence code ECO:0000245 (RCA) Issue: no entry in the With/From field Need manual review to see if they can be changed to an experimental code If not, delete the annotation How many of these and who? AgBase - 4 GR - 17 @jaiswalp

[vanaukenk]

TAS

Annotations to GO:00046983 (protein dimerization activity) and evidence code ECO:0000304 (TAS) Issue: no entry in the With/From field Need manual review to see if they can be changed to an experimental code If not, delete the annotation How many of these and who? ~DFLAT - 1~ @vanaukenk GeneDB - 4 @uliboehme ~MGI - 2 (fixed)~ ~RGD - 3 (fixed)~ UniProt - 3

[jaiswalp]

please delete these annotations GR - 17

[hattrill]

FB done

[sabrinatoro]

ZFIN annotations made with IDA have been changed.

@pgaudet @vanaukenk : Just to make sure: I should ask the ZFIN developers to update the other "protein dimerization activity" annotations to "protein binding" (with IPI). Is that correct (this is happening at the Mod)? Is there a ticket where this work should be reported when done? Thanks!

[vanaukenk]

@sabrinatoro

Yes, the ZFIN developers can update 'protein dimerization activity' annotations that use IPI to 'protein binding'. The full set of recommendations for this terms is in this Google doc (in the annotation review folder): https://docs.google.com/document/d/1JxzNwl1fr5Fj-IJy_Fo1lLfAlAQB8IxPDwwYKxIXBZo

Let us know if you have any other questions.

[pfey03]

done with Dicty, older paper not sure who annotated, extracellular matrix proteins form different disulfide bonds , but annotated to 'extracellular matrix structural constituent' that covers it ok.

[RLovering]

UCL done

[pgarmiri]

UniProt-EBI annotations have been checked and actions recorded in the spreadsheet. SWIS and SWIP annotations are tagged.