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GO and PROSITE

Xinghua Lu xlu at cbmi.upmc.edu
Thu Apr 4 15:15:17 PST 2002


Dear all ,

Thank for the quick response from Wolfgan and Rolf.  We have a local GO
running and can query the database.  As we can see that a sequence from the
database have more GO terms than PROSITE patterns associate with it.  We
found out that average ratio of GO:PROSITE per sequence is 3:1.  The
question is which one of the multiple GO terms has exactly same (or closely
related) meaning as the annotation of PROSITE.  In another word, it is to
map GO terms with PROSITE pattern correctly.  It will be nice for the
database, when queried with a GO term, to return a sequence pattern that
encode the function for that GO term, or vice versa.

We have tried different methods to associate the GO term with PROSITE
patterns.  The result is interesting and promising. However, for most of
time,  the GO term tends to be over generalized than the annotation of
PROSITE pattern.  We need some "gold standard" to evaluate our result.
Alternatively, we can make our system available on the web and have
friends at geneontology evaluate the results.  Eventually, if the system works
well, it can be part of GO.  I hope this will be of interest?  Suggestions
please.

Best regards,

Xinghua Lu
M.D., Ph.D
Center for Biomedical Informatics
Unversity of Pittsburgh



----- Original Message -----
From: "Wolfgang Fleischmann" <iwfl at mac.com>
To: "Xinghua Lu" <xlu at cbmi.upmc.edu>
Cc: <gofriends at geneontology.org>; <goa at ebi.ac.uk>
Sent: Friday, April 05, 2002 1:44 PM
Subject: Re: GO and PROSITE


> Hi Xinghua,
>
>
> On Friday, April 5, 2002, at 07:24 , Xinghua Lu wrote:
> > 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?
>
> PROSITE is part of InterPro, see www.ebi.ac.uk/interpro for details.
> Nicky Mulder started to map InterPro entries to GO terms. As all PROSITE
> patterns have exactly one InterPro accession, her mapping can be
> translated
> easily from InterPro -> GO to PROSITE -> GO. If you have difficulties
> doing
> that, mail again, we surely can help with that.
>
> Similarily, searching for PROSITE patterns is part of searching for
> InterPro
> entries. You can use this online or download and install at your site.
> "InterProScan"
> has an option to do the mapping to GO terms. Input is a aminoacid
> sequence,
> output are GO terms.
>
> >  Another question, is there such association that can be used
> > as "golden standard" for me to evaluate my result?  Thanks a lot in
> > advance.
>
> Well, I don't know if we claim to be the standard, but Nicky's
> interpro2go mapping
> is done manually and carefully inspected.
>
> To retrieve the InterPro to GO mappings, go either to
> www.ebi.ac.uk/interpro and
> follow the link to 'List of InterPro to GO mappings", or go to
> www.geneontology.org
> and scroll down to 'Indices of other Classification systems to GO'.
>
> Cheers,
> Wolfgang
>
>
> Wolfgang Fleischmann
> EMBL Outstation - The EBI       e-mail: fleischmann at ebi.ac.uk
> Wellcome Trust Genome Campus     phone:    +44 (0)1223 494406
> Hinxton, Cambridge CB10 1SD, UK    fax:    +44 (0)1223 494468
>


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