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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:0010737 protein kinase A signaling & regulation children #4961

Open pgaudet opened 7 months ago

pgaudet commented 7 months ago

Check annotations to GO:0010737 protein kinase A signaling

Annotations are here: https://docs.google.com/spreadsheets/d/12PMtUTxC4FMVGkyH5drkMi3i30v1K_Q7uhL_lJ-MSbQ/edit#gid=0

AgBase | 1 ARUK-UCL | 10 BHF-UCL | 5 CAFA | 3 dictyBase | 7 FlyBase | 4 MGI | 12 ParkinsonsUK-UCL | 1 RGD | 2 SGD | 9 UniProt | 17

deustp01 commented 7 months ago

Reactome has one use, R-HSA-163358, not listed above but the proposed change #26899 is OK with us.

pgaudet commented 7 months ago

@deustp01 I did not get this mapping when I ran the query: https://github.com/geneontology/go-annotation/blob/master/reports/4961/EMPTY_mappings_GO_0010737.tsv

The likely explanation is that this mapping is not in theReactome2GO mapping file: http://release.geneontology.org/2024-01-17/ontology/external2go/reactome2go

Do you know why this one is missing? As far as I know we take mappings from Reactome. Is this file out of date?

@balhoff Aren't Reactome mapping injected in the ontology and re-exported as mappings?

Thanks, Pascale

deustp01 commented 7 months ago

Quick sloppy answer without investigating this instance: we have put a lot of restrictions on what Reactome annotations can be used to generate a GAF file, to prevent things like propagation of the MF term assigned to the gene product that enables a reaction also onto gene products that happen to be participants in the reaction. Also, when the catalyst of a reaction is a multi-protein complex and we have not identified the single gene product member of the complex that is the active unit, we make no GAF entries, to prevent assigning an MF term to the indirectly-contributing complex members.

Work now underway on our GO-CAMs will eventually yield a GAF and GPAD export that does a better job of handling these limitations to recover more information. That should be done soon-ish, so it's probably not worth the effort to make additional tweaks to our current GAF-generating script. Meanwhile, as here, I can reliably find Reactome content affected by a proposed GO change by looking in our internal database for all uses of the affected GO term. That is reliable but also the reason I have trouble with long lists of affected GO terms. @ukemi

pfey03 commented 7 months ago

@pgaudet Is there any replacement? Petra

pgaudet commented 7 months ago

Hi @pfey03

I will create the new cAMP-PKA signaling term, plus regulation, and once that done, people can review their annotations.

Thanks, Pascale

pfey03 commented 7 months ago

@pgaudet ok, this works well for us as the PKA is downstream of cAMP and even in the main paper they say cAMP dependent PKA. Let me know when the new GO terms are ready to use in P2GO; I also wait for the new term

RLovering commented 7 months ago

I'm going to wait until there is a new term before reviewing - hope that is OK

LiNiMGI commented 2 months ago

MGI done.

hattrill commented 1 month ago

FB done

RLovering commented 1 month ago

UCL done

suzialeksander commented 1 month ago

GO:0019933 cAMP-mediated signaling is the new term, see also https://github.com/geneontology/go-annotation/issues/4960. Can you please check annotations @Antonialock @sylvainpoux @pfey03 @srengel @slaulederkind

srengel commented 3 weeks ago

SGD done.