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Review annotations to beta catenin #1714

Closed hattrill closed 6 months ago

hattrill commented 6 years ago

Hi @RLovering, @slaulederkind, @ukemi, @pgarmiri

I have some annotation issues for beta catenin that I would like you to review as part of the signaling project.

  1. Could you please review some annotations to beta catenin. Beta catenin does not directly bind DNA, but interacts with regulatory regions via other transcription factors, TCF/LEF being the major factor. Could you review your annotations to: DNA binding transcription factor activity and DNA binding terms and their children? Suggested replacements:RNA polymerase II transcription coactivator activity GO:0001105 and/or RNA polymerase II transcription factor binding GO:0001085

  2. As beta catenin acting as a coactivator in the nucleus is a hallmark of the canonical wnt signaling pathway that distinguishes it from non-canonical pathways, it would seem appropriate to upgrade all annotations made to "Wnt signaling pathway" GO:0016055 to the more specific term "canonical Wnt signaling pathway GO:0060070

The annotations can be found in this spreadsheet: https://docs.google.com/spreadsheets/d/1WJHkgtXLvPizEJt5Sce8mFeH9AI_JUAtQa0pVOmAH_w/edit#gid=0

Grand totals for manual annotations: BHF-UCL 1 -done ParkinsonsUK-UCL 2 - done MGI 11 RGD 13 - pending MGI updates UniProt 9 - done

Please reassign if you wish, Thanks, Helen

pgarmiri commented 6 years ago

The UniProt annotations are also fixed. Thanks, Penelope

slaulederkind commented 6 years ago

All of the RGD annotations are ISO or ISS, assigned by import pipelines. When MGI changes their annotations, the RGD annotations will be corrected by the import pipeline.

hattrill commented 6 years ago

Thanks @pgarmiri. Can I get you to do one more fix? P18824-1, PMID:9635189 (it's a Dmel one that I missed off) to upgrade from Wnt signaling pathway GO:0016055 to canonical Wnt signaling pathway GO:0060070. Here's the link to the P2GO page:https://www.ebi.ac.uk/internal-tools/protein2go/dynamic.html?database=production#ac=9635189

pgarmiri commented 6 years ago

Hi @hattrill , update is done. If you find any more, just let me know.

ukemi commented 6 years ago

I'm pretty sure I caught all the MGI ones.

hattrill commented 6 years ago

Brill, thanks @ukemi

ukemi commented 6 years ago

Note, I will also change our annotations from ChIP experiments from 'chromatin binding' to 'chromatin' as was recently decided.

pgaudet commented 6 years ago

@hattrill Is this resolved ?

hattrill commented 6 years ago

Hi @vanaukenk - must have missed this before, there is one WormBase one: WB:WBGene00000238 Bar-1 Wnt signaling pathway IMP PMID:11560894 that you might be able to upgrade to canonical.

pgaudet commented 5 years ago

@vanaukenk Can you have a look at that annotation ?

WB:WBGene00000238 Bar-1 Wnt signaling pathway IMP PMID:11560894 that you might be able to upgrade to canonical.

After that is fixed this ticket can be closed.

Thanks, Pascale