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[Gofriends] Best practice for integration of GO annotation ?

Midori Harris midori at
Wed Mar 4 04:03:43 PST 2009


Thank you for your interest in GO. Although the OBO format version of GO 
is authoritative, if you need only term names and IDs, we have a simple ID 
-> name, ontology mapping file available:

Tab-delimited flat files of GO annotations from the GO repository from 
this web page:

Or, if you prefer, the same files are available by FTP and anonymous CVS, 
as described here:

The file format is documented here:


Midori A. Harris, Ph.D.
GO Editor
Wellcome Trust Genome Campus
Cambridge CB10 1SD UK

Tel: +44 (0) 1223 494667
Fax: +44 (0) 1223 494468
Email: midori at

On Wed, 4 Mar 2009, K. Shameer wrote:

> Hello GOFriends,
> I am looking for a best-practice method used by GO friends for integration
> of GO annotation for genes in model organism. I need to store the GO data
> for several model organisms in a local databases and retrieve the
> annotation as a part of a web server based on requirement. I obtained GO
> IDs using BioMart, using the GO IDs, I tried different perl modules to
> obtain GO term from ID, but I find the processing is really slow - its
> taking approximately 15 seconds to get term using a GO ID. Is there a
> better approach to get the Gene ID, GO ID, GO Terms for model organisms as
> a flat file ? I am also curious to know how GO friends obtain GO
> annotations for genomes of interest - any best practices ?
> Thanks in advance,
> Khader Shameer
> Bangalore
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