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Review annotation for GPCR #1691

Open pgaudet opened 6 years ago

pgaudet commented 6 years ago

Note that there are multiple terms to review, so multiple spreadsheets

GO:0030817 regulation of cAMP biosynthetic process DONE https://docs.google.com/spreadsheets/d/16bL-BHUIoljKbcuCwDdGd24VWJ-rfBtmT-2Ouve4Nrs/edit#gid=0

GO:0030819 positive regulation of cAMP biosynthetic process https://docs.google.com/spreadsheets/d/16bL-BHUIoljKbcuCwDdGd24VWJ-rfBtmT-2Ouve4Nrs/edit#gid=0

GO:0030818 negative regulation of cAMP biosynthetic process https://docs.google.com/spreadsheets/d/1rZXktSSZhhRUXMgpXKgr5wrlk8XIB4w6ZOPzQLvK8Mc/edit#gid=0 Total annotations: 144 0 InterPro 32 EXP, mostly GPCRs Please review and move to 'adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway' if appropriate

I will move this part in a new ticket GO:0045762 positive regulation of adenylate cyclase activity https://docs.google.com/spreadsheets/d/1pyiNa7oPdYWUXkf3QsnGs4_-YQcJgKrIIwxNQKErFDM/edit#gid=0

Please review and move to 'adenylate cyclase-activating G protein coupled receptor signaling pathway' if appropriate

GO:0043950 positive regulation of cAMP-mediated signaling https://docs.google.com/spreadsheets/d/1PHr1ONPFj3N08GIdWouNxTGr2BZCdTPZm3eIegt-lcg/edit#gid=0 Please review and move to 'adenylate cyclase-activating G protein coupled receptor signaling pathway' if appropriate

GO:0007194 negative regulation of adenylate cyclase activity https://docs.google.com/spreadsheets/d/1H6H1V-0v4-_-uf9WZ8MsTEdtM9yhM2wUpfrlK98ZYe8/edit#gid=0 Total annotations: 563 0 InterPro 30 EXP, mostly GPCRs Please review and move to 'adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway'  if appropriate

pgaudet commented 6 years ago

The Noctua model for the adenylate cyclase activating G-protein-coupled receptor signaling pathway is here: http://noctua.berkeleybop.org/editor/graph/gomodel:59dc728000000351?barista_token=6w9kdeoar5loe2v7jc9s

BarbaraCzub commented 6 years ago

Hi @pgaudet could you please explain why these regulation terms are not appropriate? What guidelines should we follow, when deciding whether a term is appropriate or not? I see that the topic 'Review cAMP-mediated GPCR signaling pathway annotations' was discussed on the annotation call today, but the minutes do not appear to have been updated to explain what's been decided, and what should be done. Thanks!

RLovering commented 6 years ago

Hi

As there seem to be lots of different relations to choose and it is not clear how these relations will be translated into annotations I have looked at the annotations that are created by the above model. I am surprised to find that the FSHB (the ligand) and FSHR (the receptor) both have 'part_of(adenylate cyclase-activating G-protein coupled receptor signaling pathway)' in the AE field. As well as several preceded_by relations (which don't make sense to me and also confuse me because I thought the GOC had agreed to aim to create forwards annotations and preceded_by implies backwards annotations).

However, there are no actual 'normal' annotations created which associated the GO term adenylate cyclase activating G-protein-coupled receptor signaling pathway with the ligand and the receptor.

Plus I am not sure that negative regulation terms are likely to be 'part_of' the adenylate cyclase activating G-protein-coupled receptor signaling pathway.

Thanks

Ruth

ValWood commented 6 years ago

I agree that the relations are unintelligible . However I think the part_of relation of the ligand & receptor to the pathway is because it is hard coded in the model (hopefully regulates don't automatically get converted to part_of?).

(I thought the receptor was part of the pathway?)

vanaukenk commented 6 years ago

@BarbaraCzub - the minutes are now available for the call: http://wiki.geneontology.org/index.php/Annotation_Conf._Call_2017-11-14 Please check and let us know if you need further clarification. Thx.

RLovering commented 6 years ago

Barbara tells me that the process annotation was not included as there was no evidence, however we are unable to get onto noctua to confirm this

RLovering commented 6 years ago

Please would you confirm what you mean by the statement (in the minutes): "Perhaps there is ‘direct’ negative regulation of ACA activity’, let’s see when we review the annotations." Are you saying that any proteins which ‘directly’ negatively regulate ACA activity, should be annotated as 'ACA inhibitor activity', or that this would imply that the term 'negative regulation of ACA activity’ should be kept if there are examples of 'direct regulation' (ie by binding)?

Thanks

Ruth

sabrinatoro commented 6 years ago

@pgaudet : I have reviewed the ZFIN annotations to GO:0030819 positive regulation of cAMP biosynthetic process.

[also: some of these annotations came from GOA (and were not made by a ZFIN curator). What should I do in order to get these annotations updated? IF I remove them from ZFIN, they will be brought back through the next GOA load.]

vanaukenk commented 6 years ago

I checked our WB annotation to:

GO:0007194 negative regulation of adenylate cyclase activity

We've annotated a phospholipase C to this term and it is believed to reduce adenylate cyclase activity via competitive binding of an adenylate cyclase activator, Ha-Ras.

I will leave this annotation for now, but we could discuss on the next annotation call whether we all agree that this is a case of negative regulation.

PMID:9497345 WB:WBGene00004036 UniProtKB:G5EFI8

pgaudet commented 6 years ago

Hi everyone,

Can you provide put the protein + PMID for the annotations you could not rehouse ?

Thanks, Pascale

hdrabkin commented 6 years ago

For GO:0007194, PMID:16386234 suggests that Palm negatively impacts cAMP independent of coupling to adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (effects both dopamine receptor-activated as well as receptor-independent generation of cAMP

hattrill commented 6 years ago

@pgaudet I've dealt with the FB ones, apart from Gprk2 (P32866) GO:0043950 positive regulation of cAMP-mediated signaling. Not sure how to re-house this at the moment as not sure of the mechanism - might be via GPCR or via smoothened pathway and/or Galphai coupling.

sabrinatoro commented 6 years ago

Annotations from GOA to update (or remove, and I'll create these annotations in ZFIN):

Also:

Since I do not how how to update the "positive/negative regulation of adenylate cyclase-activating G-protein receptor activity" annotations (whether new terms are required or not), I am leaving my name assigned to this ticket.

BarbaraCzub commented 6 years ago

GO:0007194 negative regulation of adenylate cyclase activity Total annotations: 563 0 InterPro 30 EXP, mostly GPCRs Please review and move to 'adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway' if appropriate (3) ARUK-UCL

The ARUK-UCL annotations to the term 'GO:0007194 negative regulation of adenylate cyclase activity' are based on PMIDs: 20141570 and PMID:18723082.

It appears appropriate to use the term 'adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway' to update the annotations for both PMIDs because FPR2, involved in experiments shown in both papers, in theory is a G-protein coupled receptor. I have done this now.

Antonialock commented 6 years ago

pombase should be done now

hdrabkin commented 6 years ago

GO:0030818 negative regulation of cAMP biosynthetic process done for MGI

pgaudet commented 6 years ago

@sabrinatoro Looking at the paper it looks like mc4r should be annotated to 'G-protein coupled receptor protein signaling pathway' and the accessory proteins to either 'regulation of G-protein coupled receptor protein signaling pathway' and/or 'G-protein coupled receptor regulator activity' (this term does not seem to exist yet).

Pascale

ggeorghiou commented 6 years ago

Hi Pascale,

For CAFA, the evaluation of the submissions is in progress. I do not want to change these annotations yet since they are being used for evaluations. I'll review them and change them as soon as the evaluation is done. As for UniProt annotations, we have to figure out which belong to us at EBI and belong to the curators at SIB. So this could take a little bit of time for us to go through.

Best,

George

hdrabkin commented 6 years ago

Finished GO:0043950 positive regulation of cAMP-mediated signaling; annotations to + and - regulation of above (two isoforms). Currently only 'positive regulation adenylate cyclase-activating G protein coupled receptor signaling pathway'; will wait until I create the neg reg term

pgaudet commented 6 years ago

Need to add regulation of 'adenylate cyclase-activating G protein coupled receptor signaling pathway' 'positive regulation adenylate cyclase-activating G protein coupled receptor signaling pathway' 'negative regulation adenylate cyclase-activating G protein coupled receptor signaling pathway'

pfey03 commented 6 years ago

Finished cAMP biosynthetic process terms: GO:0030819 positive regulation of cAMP biosynthetic process (3) GO:0030818 negative regulation of cAMP biosynthetic process (1 + 2 PAINT) GO:0030817 regulation of cAMP biosynthetic process ( 1 not explicitly requested but is at least equally wrong)

hattrill commented 6 years ago

Hi @pgaudet btw: if no-one else feels the need for "GO:0043950 positive regulation of cAMP-mediated signaling", I am not absolutely wedded to it. If it is standing in the way of moving forward, I will dump it - it is, after all, just one annotation.

pfey03 commented 6 years ago

Took care of all, I hope.

sabrinatoro commented 6 years ago

The ZFIN annotations have been updated. @pgaudet : please note that the following annotations came from GOA via load, and will have to be deleted on the GOA side (otherwise, they will be brought back with the next load). I have created the correct annotations, so the following annotations could be deleted (instead of updated): mc4r GO:0030819 ZFIN:ZDB-PUB-130805-10|PMID:23869017 IDA mrap2b GO:0030819 ZFIN:ZDB-PUB-130805-10|PMID:23869017 IMP

pgaudet commented 6 years ago

@ggeorghiou @pgarmiri Can you please have a look at the annotations mentioned by @sabrinatoro

mc4r GO:0030819 ZFIN:ZDB-PUB-130805-10|PMID:23869017 IDA mrap2b GO:0030819 ZFIN:ZDB-PUB-130805-10|PMID:23869017 IMP

Thanks, Pascale

pgarmiri commented 6 years ago

Hi, There are also 4 EXP annotation to GO:0030817 'regulation of cAMP biosynthetic process' that could be reviewed as well.

The UniProt annotation has been revised already.

(There are also 16 EXP annotation to GO:0043949 'regulation of cAMP-mediated signaling' that we might want to verify.) Thanks, Penelope

pgarmiri commented 6 years ago

Hi @pgaudet , I had a look at the annotations you mentioned, as George is at a course these couple of days. The annotations have been created by SIB, so I can't update/ delete them. @sylvainpoux could you please take a look at those? Thanks, Penelope

srengel commented 6 years ago

i just rehoused the 3 SGD annotations under the other suggested term.

hdrabkin commented 6 years ago

GO:0030819 is taken care of for MGI One not changed as authors state not sure of mechanism (PMID:15632412) for Avp

bmeldal commented 6 years ago

Our 3 GABA-B complexes were annotated to both, GO:0007194 negative regulation of adenylate cyclase activity and GO:0007193 adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway as they had no parent-child relationship. Taken out GO:0007194.

updated 21 annotations to GO:0043950 positive regulation of cAMP-mediated signaling to GO:0007189 adenylate cyclase-activating G protein coupled receptor signaling pathway

rachhuntley commented 6 years ago

Hi,

There is one miRNA annotated to "negative regulation of adenylate cyclase activity" because it silences the ADCY6 gene affecting accumulation of cAMP - does this constitute direct regulation?

The miRNA also targets some other components of the beta-adrenergic receptor signaling pathway, and there is evidence to annotate to "adenylate cyclase-inhibiting adrenergic receptor signaling pathway involved in heart process", but I'd prefer to annotate to a negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process (which doesn't yet exist). Quote: "Altogether, these results demonstrate that miR-133 is directly involved in the modulation of the β1AR signaling pathway by acting at multiple levels downstream of β1AR (β1AR–ACVI–PKA)."

I'll leave the annotation to "negative regulation of adenylate cyclase activity" for now as an example of possible direct regulation.

URS00004C9052_10090 (miR-133a-3p) PMID:24807785

Rachael.

pgaudet commented 6 years ago

Hi all,

I created a spreadsheet for keeping track of the reviews: https://docs.google.com/spreadsheets/d/1pyiNa7oPdYWUXkf3QsnGs4_-YQcJgKrIIwxNQKErFDM/edit?usp=sharing

(apologies for doing this so late! next time I'll do it from the onset).

Please update the spreadsheet to indicate which annotations were OK, which you have changed, and which you think should remain.

Thanks, Pascale

pgaudet commented 6 years ago

Hi @rachhuntley Nice example ! It seems OK to leave it as "negative regulation of adenylate cyclase activity" for now (I would not say it's direct but for BP it's OK according to our current guidelines)

Thanks, Pascale

rachhuntley commented 6 years ago

Hi Pascale, Do you want me to add this to the spreadsheet or are you only interested in the protein annotations? Rachael.

pgaudet commented 6 years ago

You can add it to the spreadsheet, yes.

Thanks, Pascale

pgarmiri commented 6 years ago

Hi, I have updated the UniProt annotations that I could.

pfey03 commented 6 years ago

I've now updated all Dicty annotations and added it to spreadsheet

pgaudet commented 6 years ago

Hello @sabrinatoro @sylvainpoux @suzialeksander We're still missing your reviews for https://docs.google.com/spreadsheets/d/16bL-BHUIoljKbcuCwDdGd24VWJ-rfBtmT-2Ouve4Nrs/edit#gid=0

I will proceed with obsoletion of 'regulation of cAMP biosynthetic process' and its positive and negative children this week.

Thanks, Pascale

sabrinatoro commented 6 years ago

@pgaudet : All the ZFIN annotations were reviewed (see my comment from Dec 4th). Is there something I am missing?

sabrinatoro commented 6 years ago

@pgaudet The review spreadsheet didn't exist when the review was done. I updated the document. Please let me know if there is more that should be done.

pgaudet commented 6 years ago

Thanks @sabrinatoro - it's all good :)

vanaukenk commented 6 years ago

The WB annotation to 'negative regulation of adenylate cyclase activity' is now removed.

pgaudet commented 6 years ago

Status cAMP biosynthetic process annotations:

1. GO:0030819 positive regulation of cAMP biosynthetic process https://docs.google.com/spreadsheets/d/16bL-BHUIoljKbcuCwDdGd24VWJ-rfBtmT-2Ouve4Nrs/edit#gid=0

2. GO:0030818 negative regulation of cAMP biosynthetic process https://docs.google.com/spreadsheets/d/1rZXktSSZhhRUXMgpXKgr5wrlk8XIB4w6ZOPzQLvK8Mc/edit#gid=0

The terms are now obsoleted https://github.com/geneontology/go-ontology/issues/14718

Thanks, Pascale

rachhuntley commented 6 years ago

Updated the miRNA annotation.

pgarmiri commented 6 years ago

The CAFA annotations have been updated. I can't find any annotations to GO:0030818 negative regulation of cAMP biosynthetic process, so I assume they are all fixed too...

pgaudet commented 6 years ago

Hi @pgarmiri There is one remaining annotations to Q922S4 (MGI:MGI:2446107)

Thanks, Pascale

pgarmiri commented 6 years ago

right @pgaudet , I had a look at this protein and I found one ISO annotation (assigned by MGI) from the human entry that was ours. I have updated the human entry, so that should be fixed eventually. Is this one you had in mind? Thanks, Penelope

pgaudet commented 6 years ago

yes @pgarmiri , thanks !

RLovering commented 5 years ago

Hi Pascale

row 316 BHF annotation had been removed previously but not marked on sheet. rows 201 and 473 Parkinsons's UK these were changed to GO:0007189 adenylate cyclase-activating G protein-coupled receptor signaling pathway in 2017, not sure why these are listed as in progress on the spreadsheet

Ruth