Review annotations to GO:0051259 'protein complex oligomerization' and children

[vanaukenk]

Following on from the 2019-06-11 annotation conference call, we are asking groups to review their annotations to GO:0051259 'protein complex oligomerization' and children terms.

This review is in preparation for obsoletion of these terms in the ontology as capturing the stoichiometry of protein interactions is not within the scope of GO.

Guidelines for how to review and updates annotations to these terms are in the first section of this document on the GO's Google drive.

The full spreadsheet, with tabs for both manual experimental and sequence-based annotations, is here: https://docs.google.com/spreadsheets/d/15tIvSts5PcWidtMpXTQQfjFY3LTYcfjOc62Y5_FeRpU

Please comment in this ticket if you have any questions about existing annotations.

Contributor (Assigned by)

Experimental

Sequence

Assignees are listed to the right; please remove your name once you've finished reviewing the annotations. Thank you!

Also, for GeneDB annotations: @uliboehme

[hattrill]

FB done

[srengel]

SGD done.

[tberardini]

@ebakker2 Can you please look at the TAIR annotations? Thanks.

[pfey03]

dictyBase done

[keseler]

EcoCyc done

[sabrinatoro]

I came across a lot of "oligomerization" annotations based on crystallography information.
The information in the publications are: 1) authors mentioning that the proteins exist as trimer/tetramer/..., 2) crystallography analysis of the trimer/tetramer/... There is actually no reported binding experiments. I am tempted to remove these annotations, but I wanted to make sure this is the correct thing to do. Thank you! @vanaukenk @pgaudet

[pgaudet]

@sabrinatoro

Thanks for reporting this. We did decide that the oligomeric state was outside the scope of GO, so deleting would be correct (unfortunately!)

Pascale

[sabrinatoro]

Thank you @pgaudet. ZFIN annotations have been reviewed.

[EricaBakker]

TAIR is done

[RLovering]

HGNC, BHF-UCL, Parkinson's-UCL, ARUK-UCL done

[gthayman]

With the help of Jennifer Smith, RGD is done.

[hdrabkin]

MGI done

[srengel]

ok SGD now really is done ;)

[vanaukenk]

@happy-lorna

As described above, we are going to obsolete the Biological Process terms that describe oligomerization of gene products, as capturing this information is no longer within the scope of GO annotation.

I've added the existing InterPro2GO mappings that use these terms in a separate tab of the annotation review spreadsheet: https://docs.google.com/spreadsheets/d/15tIvSts5PcWidtMpXTQQfjFY3LTYcfjOc62Y5_FeRpU/

We recommend that all of these mappings be removed.

Let me know if you have any questions.

Thanks!

[pgarmiri]

Hi, All UniProt-EBI annotations have been reviewed and actions recorded in the spreadsheet. SWIS and SWIP annotations have been tagged. Thanks, Penelope