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GO and PROSITE

Chris Mungall cjm at bdgp.lbl.gov
Sat Apr 6 17:28:33 PST 2002


You can also do this in SQL by connecting to the GO database in directly -
if you click on the "example SQL queries" link in
http://www.godatabase.org/dev/database

you can see some examples for doing aggregate queries grouping either
prosite/pfam etc or interpro with go terms, finding common paired
patterns. You can also queries the interpro2go links directly.

i wrote a quick script to see if there could be any gains in looking
directly at correlations between go terms and the contributing interpro
dbs rather than interpro directly, and it turns out that there isn't. So
like Rolf says, best just go with interpro2go.

On Fri, 5 Apr 2002, Rolf Apweiler wrote:

> Hi Xinghua,
> PROSITE is an InterPro member database. Nicola Mulder here at EBI has done a
> mapping of InterPro entries to GO. See
> ftp://ftp.ebi.ac.uk/pub/databases/interpro/interpro2go or
> ftp://ftp.geneontology.org/pub/go/external2go/interpro2go. With a simple SRS
> query you can do what you wanted: associate PROSITE patterns directly with GO
> terms
>
> I will send you the results file of the SRS query separately, since I do not
> want to send it such a monster file to the whole mailing list.
>
> Cheers
>
> Rolf
>
>
> =======================================================================
> Rolf Apweiler                           | SWISS-PROT Coordinator
> EMBL Outstation                         | Email:apweiler at ebi.ac.uk
> European Bioinformatics Institute (EBI) | URL:  http://www.ebi.ac.uk
> Wellcome Trust Genome Campus, Hinxton   | Tel:  +44 (1223) 494435
> Cambridge CB10 1SD, UK                  | Fax:  +44 (1223) 494468
> ========================================================================
>
>
>
> > Hi everyone,
> >
> > The current GO sequnce files have PROSITE and other sequence patterns
> > associated with them.  I am try to develop a method to associate the GO term
> > with PROSITE patterns directly.  In another word, assign a GO term to the
> > patterns, so that people can search the GO for patterns too.  Has this been
> > done by anyone? Another question, is there such association that can be used
> > as "golden standard" for me to evaluate my result?  Thanks a lot in advance.
> >
> > Cheers,
> > Xinghua Lu
> > M.D., Ph.D
> > Center for Biomedical Informatics
> >
> > --
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>
> --
> This message is from the GOFriends moderated mailing list.  A list of public
> announcements and discussion of the Gene Ontology (GO) project.
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