search

geneontology / go-site

A collection of metadata, tools, and files associated with the Gene Ontology public web presence.
http://geneontology.org
BSD 3-Clause "New" or "Revised" License
45 stars 89 forks source link

human proteome #819

Closed kltm closed 5 years ago

kltm commented 6 years ago

From @ValWood on September 23, 2018 7:25

How do I access the exact human reference proteome dataset that is currently used by GO?

Is this it? https://www.ebi.ac.uk/reference_proteomes

@Antonialock if so we should use this one, as it should align with GO

Thanks,

Val

Copied from original issue: geneontology/helpdesk#161

kltm commented 6 years ago

From @ValWood on September 23, 2018 7:28

Except that it has fragments, and pseudogenes, and it doesn't seem straightforward to access the HGNC IDs

kltm commented 6 years ago

@ValWood That's a good question. Honestly, if it's not an upstream or derived file and not accessible via metadata in the GAFs (then available in AmiGO or SPARQL), I'm not sure how you'd get at it. Can you think of any way of filtering down to the data that you want?

kltm commented 6 years ago

From @Antonialock on September 25, 2018 1:16

This is the ticket I was referring to in our email exchange Val

kltm commented 6 years ago

From @ValWood on September 25, 2018 5:16

OK I totally forgot that I opened this ticket. Anyway @Antonialock we will proceed with the dataset you are using now. We'll keep this one open as I need to know for the GOC discussion http://wiki.geneontology.org/index.php/2018_Montreal_GOC_Meeting_Agenda representing complete proteomes

I guess the question is, is this the set of human uniprot accessions that can be submitted?

@selewis

related ticket https://github.com/geneontology/go-annotation/issues/2082

ValWood commented 5 years ago

closing...it was for https://royalsocietypublishing.org/doi/10.1098/rsob.180241