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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:0030374 nuclear receptor coactivator activity #5502

Open pgaudet opened 3 weeks ago

pgaudet commented 3 weeks ago

Dear all,

The proposal has been made to obsolete GO:0030374 nuclear receptor coactivator activity and replace by parent GO:0003713 transcription coactivator activity

Ontology ticket: https://github.com/geneontology/go-ontology/issues/29150

Annotations are here: https://docs.google.com/spreadsheets/d/1Yh2NnXh5Rg1V9rPr3-TCz1xRQnWHM9O4kL7l-JDYKl0/edit?gid=0#gid=0

pgaudet commented 3 weeks ago

InterPro and UniRule/HAMAP annotations need to be moved up to the parent.

pgaudet commented 2 weeks ago

@colinlog and I have reviewed the annotations in the spreadsheet. We have found no co-activator specific for nuclear receptors (although some have very little evidence). So, it would be OK to move all annotations to the parent term transcription coactivator activity.

All groups impacted should have their annotations automatically migrated:

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AgBase | 1 -- | -- ARUK-UCL | 6 - done BHF-UCL | 6 - done FlyBase | 4 GO_Central | 6 MGI | 14 ParkinsonsUK-UCL | 2 - done RGD | 6 UniProt | 41

pgaudet commented 2 weeks ago

Mappings: move to parent transcription coactivator activity

pgaudet commented 2 weeks ago

@slaulederkind

There is one annotation that we don't agree with: RGD:3611 Rxrb is a dbTFF, but it's part of a complex, so sometimes the terminology used by authors is confusing. It's not a 'co-activator' in the sense that GO means.

Can you please review and change the annotation?

Thanks, Pascale

slaulederkind commented 2 weeks ago

@pgaudet From the definition for "nuclear receptor activity" (GO:0004879), "...When the nuclear receptor functions by binding to other transcription factors or transcription factor complexes, consider instead annotating to 'GO:0030374 ; nuclear receptor transcription coactivator activity' or GO:0140536 ; nuclear corepressor activity, it looks like "nuclear receptor coactivator activity" (GO:0030374) would be appropriate.

pgaudet commented 1 week ago

Thank you ! I'll fix this

sarach06 commented 1 week ago

Hi Pascale, Thank you for this. I have replaced the term with the parent term in the InterPro entries you listed. Please let me know if additional changes or mappings should be done in the future. These changes will be available in InterPro 103.0. Also, just a reminder so we don't miss tickets in the future, please add the InterPro mapping label apart of the assignees if possible, so they are found easily. Thanks!

Best wishes, Sara