Finding the right GO annotation flat file for human build GCRh37

Question

[summerela]

I found a download for the latest version of the GO annotation flat file here.

But I'm also trying to locate a version that goes with the GRCh37 build, and I cannot figure out how to tell which archived GO database to use. I have not heard back from their support.

Is it safe to assume that a GO database release in February 2014 corresponds to Ensembl 75/GRCh37 since they are both released on the same date?

I would really appreciate it if anyone can point me in the right direction. Thanks!

[Pierre Lindenbaum]

what's the specific link between GOA and GRCh37 ?

[summerela]

I see what you mean there!

I guess more specifically, I need to figure out which version of Uniprot was used? I'm new to working with a species that actually has a reference so please excuse my newbie-ness; if they mapped the GO terms to a version of uniprot based on GRCh37 vs a version of uniprot based on GRCh38, wouldn't that make some positional differences?

Answer 1

[Jean-Karim Heriche]

If you need GO annotations for Ensembl genes, just get them from Ensembl for the specific version you're interested in. You can do so using BioMart or the API. Uniprot-GOA is not concerned with a reference genome, it annotates protein sequences and other resources like Ensembl do the mapping to a reference genome. So if you want to use GO terms associated with some Uniprot IDs and need to map those to a particular reference then just find which genes the Uniprot IDs are associated with in the reference genome you're interested in.

[summerela]

This all makes complete sense. It doesn't matter the build, because the protein is the final product, no matter what the location on the genome. Thanks so much!