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genome ontology searching

Daniel Barrell dbarrell at ebi.ac.uk
Wed Dec 18 02:06:14 PST 2002


Murad Nayal wrote:
>>The (kludgy) way we do it is by the simple mapping: SwissProt id ->
>>SwissProt keyword -> GO term -> GOid
>>We parse the SwissProt ids from the definition lines of the blast hits
>>and use them to get to the keywords. There is a SwissProt keyword to GO
>>term mapping available on www.geneontology.org.
>>This is all done in Perl and was pretty straightforward to write. I'd
>>share the code, but it's actually tied in to a database backend and
>>would be of little use (easier to start from scratch).

The spkw2go file is updated monthly and we check for obsoletes, secondaries etc 
before releasing it at www.geneontology.org

> was this the method used to create the gene_association.goa_sptr table
> (a mapping of swissprot/embl accessions to go terms and ids, as well as
> other xdbs) was generated at the GOA project in EBI?

Yes, as well as the other transitive mappings, interpro2go and ec2go, and of 
course not forgetting manual annotation :)

Cheers

Daniel


-- 
Daniel Barrell
EMBL - The EBI
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
Phone: +44 (0)1223 492551
Email: dbarrell at ebi.ac.uk


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