Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

genome ontology searching

Murad Nayal mn216 at columbia.edu
Tue Dec 17 08:50:04 PST 2002


> 
> 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).
> 

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?

BTW: I suppose you can use this table to map swissprot ids -> GO Ids
directly without having to go through SP keywords.

http://www.ebi.ac.uk/proteome/goa/goaHelp.html

thanks

-- 
Murad Nayal M.D. Ph.D.
Department of Biochemistry and Molecular Biophysics
College of Physicians and Surgeons of Columbia University
630 West 168th Street. New York, NY 10032
Tel: 212-305-6884	Fax: 212-305-6926

--
This message is from the GOFriends moderated mailing list.  A list of public
announcements and discussion of the Gene Ontology (GO) project.
Problems with the list?           E-mail: owner-gofriends at geneontology.org
Subscribing   send   "subscribe"   to   gofriends-request at geneontology.org
Unsubscribing send   "unsubscribe"  to  gofriends-request at geneontology.org
Web:          http://www.geneontology.org/



More information about the go-friends mailing list