Review annotations to 'GO:0000988 transcription factor activity, protein binding' and similar children

[pgaudet]

Hello,

From the annotation call of July 10, 2018, I propose to obsolete 'transcription factor activity, protein binding' and similar children. The list of terms is in the ontology ticket
geneontology/go-ontology#16053

Annotations and potential replacements for many of them are here: https://docs.google.com/spreadsheets/d/1jwgpZF3paxNOHvEHQ4v_uxOFb3FjQUOnxSJpswIzyMI/edit#gid=0

Annotation guidelines are here: https://goo.gl/dsvB18

Groups impacted | Number of annotations
BHF-UCL | 28 @RLovering - done
CACAO | 1 @sandyl27
CAFA | 11 @ggeorghiou
ComplexPortal | 3 @bmeldal
FlyBase | 21 @hattrill
MGI | 19 @hdrabkin
ParkinsonsUK-UCL | 1 @RLovering - done
PomBase | 2 @ValWood
SGD | 77 @srengel @krchristie
TAIR | 1 @tberardini
UniProt | 3 @ggeorghiou
WB | 7 @vanaukenk
ZFIN | 4 @sabrinatoro

Thanks, Pascale

[sabrinatoro]

What should I do with the following annotation?
Kctd10 was shown to bind to Tbx5a (which was shown to be a transcription factor), and this binding repress the transcriptional activity of Tbx5a.
There is no report of Kctd10 binding to DNA, and no report that it is binding to RNA polymerase II basal transcription machinery.
How should Kctd10 be annotated?
Thank you!

[pgaudet]

Hi @sabrinatoro
I would annotate to GO:0003714 transcription corepressor activity. (Note that this term needs to be reviewed too, but I am pretty sure that Kctd10 would be correctly annotated there.)

Thanks, Pascale

[pgaudet]

NOTE: I restored GO:0003711 transcription elongation regulator activity
which should allow to annotate some proteins in that list (See geneontology/go-ontology#14398)

[pgarmiri]

The UniProt annotations have been reviewed and updated.

[bmeldal]

All complexes changed. All TFs with to-be-obsoleted terms now have annotations to GO:0140110 transcription regulator activity or children. However, as the term is new I doubt all TFs in the Complex Portal are annotated with this branch... I'd have to do some archaeology to fix that!

[sandyl27]

CACAOs annotation has been updated.

[sabrinatoro]

Thank you @pgaudet.
The ZFIN annotations have been reviewed and updated.

[ValWood]

I have no annotations to GO:0000988 so I must have done them in a previous round.

[pgaudet]

@ValWood It's very possible that you already deleted the annotations, but in the spreadsheet you still have two proteins (PomBase:SPBC2D10.06; PomBase:SPBC2F12.11c)
Can you go in the google spreadsheet and mark those proteins as fixed ?
https://docs.google.com/spreadsheets/d/1jwgpZF3paxNOHvEHQ4v_uxOFb3FjQUOnxSJpswIzyMI/edit#gid=0

[tberardini]

TAIR done.

[ValWood]

done ;)

[vanaukenk]

WB annotations reviewed and updated.

[pgaudet]

@srengel @suzialeksander
Would it be OK if I went ahead with the obsoletion tomorrow, so that it appears in the next release ? (Otherwise further changes are more difficult).

That might mean you have annotations to obsolete terms but that should be for a short period until you get to fixing them.

Thanks, Pascale

[srengel]

That’s ok. I won’t be able to get to these until next week, but will get it done then.

[hdrabkin]

By the spreadsheet, any annotations left to mouse genes have been done by BHF-UCL or ParkinsonsUK-UCL; MGI can't do anything to those as they are dropped and re-loaded weekly. So I'll take my name off of the assigned.

[RLovering]

Ok BHF annotations done, but I couldn't see the Parkinson's annotation in the table, Im sure it was there before - Ruth

[pgaudet]

@RLovering
There were filters applied. There is 1 Parkinson's annotation to UniProtKB:P18848

Thanks, Pascale

[RLovering]

thanks sorted out that last one. I did try to select all in the filter option, maybe I just had slow internet
Ruth

[pgaudet]

Closing this. Some groups have not responded
@hdrabkin @hattrill @pgarmiri

but the term has already been obsoleted.

[pgarmiri]

The UniProt annotations have been reviewed and updated.

@pgaudet I had another look at the spreadsheet. There is only one annotation from UniProt left but is ISS, so this should have been fixed automatically after the parent was corrected.
Thanks

[RLovering]

Hi Pascale

in ticket https://docs.google.com/spreadsheets/d/1uHMSFAuxsOL54F0CLiB2lbrYyvjHTbyA0O2n8rsgKEI/edit#gid=0 you list BHF annotations as not done for this ticket, but they are done it is just I hadn't marked them as done. I have highlighted them on the ticket.

Ruth