How To Get Gene Ontology Ids (Go) By Using Gis?

Question

[JacobS]

Hi, I would like to annotate gene ontology IDs onto lists of GI numbers. For example, I used some software to annotate a sequence, obtained it's GI number, and now want the GO term without re-BLASTing. Also, I have over 50M such queries, so I want something that I can do locally, instead of relying on web-servers based software.

Any suggestions are appreciated! Thanks.

[Pierre Lindenbaum]

GI= gene identifier or genbank/nucleotide identifiers ?

[Neilfws]

GIs are specific to NCBI/Entrez and not especially useful for linking to anything else. If your files have some other identifier, BioMart is an option.

Answer 1

[David Westergaard]

There's a ftp available for the NCBI Gene database. You're probably interested in gene2go.gz.

edit: typo

[JacobS]

Thanks for the reply... I've downloaded and explored this file, but the vast majority of my GIs aren't found in that file. Are these the only GIs that have been associated with GOs on NCBI?

[David Westergaard]

I would believe so. GIs are just an identifier at NCBI for any gene which has been entered into the database. Probably into a very small fraction of these will have any GO annotation.

You can always lookup a few examples directly, and see if that is the case, or the file you downloaded is incomplete.