Possible sources to fix, and GO contacts list housekeeping

ValWood commented 6 years ago

based on https://github.com/geneontology/go-site/issues/807

I will update https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv

but some of these sources need to be tracked down and fixed:

[ ] 286 WormBase -> WB @vanaukenk
[x] 2 FLYBASE -> FlyBase @hattrill
[ ] 3 AGBASE -> AgBase @jinhuiz
[ ] 3 GO_CENTRAL ->@pgaudet @cmungall
[ ] 271 COLLECTF -> 5320 CollecTF? NO CONTACT PERSON , SEE BELOW

Updates to contacts file required

[x] AspGD update the group-contacts file, currently ASPGD
[x] update HGNC to Susan @sartweedie
[ ] Roslin_Institute no annotation, remove from contacts file (currently assigned to Pascale) ?
[x] change all @tonysawfordebi production to @alexsign

No contact listed in contact file, find and add

[x] 10764686 RNAcentral @AntonPetrov
[x] 325395 EnsemblMetazoa ADD for completion @alexsign
[x] 11007 EnsemblProtists " @alexsign
[x] 126 PAMGO_VMD " @pgaudet
[x] 140 SynGO-UCL " @RLovering
[x] 963 ComplexPortal @bmeldal
[ ] 1150 GONUTS (is this the correct source?) @jimhu-tamu ?
[ ] 1456 SGN ? (Solanum lycopersicum ) note many of these should be High throughput, if valid at all PMID:22903030 (def NOT IDA)
[x] 7555 CAFA @ggeorghiou
[ ] CollecTF erill (NEED GH ID)
[ ] 47 GO_Noctua @pgaudet ? @cmungall ?
[ ] 309 ASAP ?
[ ] 6 Eurofung ?
[ ] YuBioLab pengy (NEED GH ID)

Any others known?

Other updates required to contacts file:

Move the following entries to "Domain experts" section (not submitters)

[ ] Buffallo University ?
[ ] Chembl @PruMM Prudence can you give us a replacement contact GitHub ID for Chembl?
[ ] Protein Ontology ?

TBRU, this group is probably intending to submit, but we have no GitHub contact

[ ] Wikidata no annotation

ValWood commented 6 years ago

I also thought 54873 UniProtKB seemed very low for manual UniProtKB annotation, is something wrong there? @tonysawfordebi @sylvainpoux

tonysawfordebi commented 6 years ago

What are these numbers?

ValWood commented 6 years ago

That is the number of annotations with UniProtKB as submitter according to the query performed by Seth here https://github.com/geneontology/go-site/issues/807

bmeldal commented 6 years ago

I looked at the contact list and can't find Complexportal at all. I do know I added myself on a GO GH contact list a long time ago but that doesn't seems to have propagated. Should I change the file myself?

tonysawfordebi commented 6 years ago

@ValWood We're back on old ground again... there shouldn't be any annotations with UniProtKB in the assigned_by - the correct attribution is UniProt.

https://github.com/geneontology/go-annotation/issues/1772

ValWood commented 6 years ago

Hi @bmeldal I'm trying to ensure that each submitter has at least one contact in the contacts file, we only need one contact, but more than one is also OK.

You can edit the lines above with the correct details. Once all the info is collected I'll update the file so only one pull request is required. Just tick the line so I know your edits are done/approved.

ValWood commented 6 years ago

@ValWood We're back on old ground again... there shouldn't be any annotations with UniProtKB in the assigned_by - the correct attribution is UniProt.

Sigh. That's what I thought but I was so sure this was already addressed that I had misremembered what was supposed to happen. So where do the UniProtKB come from ?

tonysawfordebi commented 6 years ago

That's the $64000 question...

ValWood commented 6 years ago

I moved the UniProtKB to its own ticket ;) https://github.com/geneontology/go-annotation/issues/2072

tonysawfordebi commented 6 years ago

I saw :)

With regard to contact addresses, you can use goa@ebi.ac.uk for all the Ensembl sources and rnacentral@gmail.com for RNAcentral. Or are you looking for GH handles?

ValWood commented 6 years ago

GH handles are required for this file, so we can TAG you in tickets!

tonysawfordebi commented 6 years ago

OK - in that case, don't use me, as I'm going to be outta here in 85 days...

ValWood commented 6 years ago

So, when you go, or before we need a replacement GH handle for ALL of your entries in this file https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv Please nominate the appropriate people ;)

tonysawfordebi commented 6 years ago

Well, I'd suggest that for any kind of production-related issue tag @alexsign, and for anything that requires curator input either @ggeorghiou or @pgarmiri

Anton Petrov is probably the best contact for RNAcentral, but I can't find his GH handle...

ValWood commented 6 years ago

Anton Petrov I have it

bmeldal commented 6 years ago

Ok, I ticked myself in your original ticket and taken out the question mark. I hope that's all you need for now.

ggeorghiou commented 6 years ago

CollecTF is Ivan Erril - erill -a- umbc.edu YuBioLab is Peng Yu - pengy -a- tamu.edu Roslin Institute is managed by GOA at the moment.

pgarmiri commented 6 years ago

Hi @bmeldal , Hema's GH account should be @hbye. I think her funding for the complex portal is finished but I am sure she would be okay to look after existing annotations.

bmeldal commented 6 years ago

Ok, keep me as CP contact and if there are questions regarding Hema's annotations I'll pass them on to her.