Review annotations to GO:0006198 cAMP catabolic process

[pgaudet]

Hello,

For the GPCR work we propose to obsolete cAMP catabolic process - annotations are here:
https://docs.google.com/spreadsheets/d/1WFXwop5Meyo_vb0kYZNAT1CJaHpepLeMpk_GMEPYOPc/edit#gid=0

and impacted groups. As shown in the matrix analysis below , cAMP catabolic process phosphodiesterase activity are always co-annotated (if I got this right, @ValWood )

Contributor (Assigned by)	Curator
BHF-UCL	12
dictyBase	6
FlyBase	1
MGI	1
MTBBASE	3
PomBase	2
RGD	27
UniProtKB	15

[RLovering]

Should we make sure all of these proteins are annotated to a signaling pathway? so that they still have a BP annotation?

[pgaudet]

Right ! Interestingly most are not annotated to the pathway. This may mean that the activity was tested, outside the context of a pathway. We do need to review annotations before just moving annotations to the pathway (or its regulation).

For example the first annotation in the spreadsheet:

MGI:MGI:99555 | phosphodiesterase 4D, cAMP specific |   | GO:0006198 | BHF-UCL | NCBITaxon:10090 | IDA |  PMID:21670503

is a nice example of 'GO:0071878 negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway' (or even 'GO:0140199 negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process :)

OK ?

Thanks, Pascale

[slaulederkind]

Hey, Pascale. The spreadsheet is read only.

[pfey03]

@pgaudet I also cannot edit the table
Cannot even update them without access to the table as I cannot see gene IDs. And just by PMID is too cumbersome or to look for them by term IDs.. Please give access to us asap, as I only have short time windows right now to fix these annotations. Thanks!

[pgaudet]

Should be fixed.

Thanks,
Pascale

[slaulederkind]

RGD annotations fixed or deleted.

[RLovering]

Thanks for the annotation advice. I think the suggested term can only be applied to Pde4b, rather than Pde4d, but very helpful.
The majority of the BHF-UCL annotations were based on enzyme assays and therefore no expt evidence for role in signaling.

All BP terms removed as requested

Ruth

[hattrill]

FlyBase - done

[pgarmiri]

The UniProt annotations have been checked.

[hdrabkin]

I believe the one annotation in the spreadsheet for MGI has already been removed
Yes, it is gone

[pfey03]

Sorry it took me so long - 2 grants this year.. but now took care of all Dicty, mostly removed or changed

[ValWood]

PomBase fixed, sorry I missed this one.

There are still 7 annotations tho' (dictybase, MTBBASE, BH-UCL)

[ValWood]

ignore dictybase. (MTBBASE, BH-UCL)

[Antonialock]

MTBBASE done

[RLovering]

added the missing annotation to the spreadsheet and BHF-UCL now completely done

[pgaudet]

Out of date