[Bioperl-l] Fwd: [GMOD-devel] GO::TermFinder Announcement

[Lincoln Stein]

Hi All,

I'm forwarding this info to the BioPerl list.  There is some overlap between 
this work and the core BioPerl Onotology work, but not so much.  However, 
there may be namespace clashes, and we should audit and correct these before 
too much client code is run.

Gavin says that he sent an early version of this code to the bioperl group 
some months ago but didn't hear back.  I wasn't aware of it.

Lincoln

----------  Forwarded Message  ----------

Subject: [GMOD-devel] GO::TermFinder Announcement
Date: Sat, 8 Mar 2003 15:38:49 -0800 (PST)
From: Gavin Sherlock <sherlock at genome.stanford.edu>
To: gofriends at geneontology.org
Cc: ge-curator at genome.stanford.edu, gmod-devel at lists.sourceforge.net

Hi All,

	Under the auspices of the GMOD grant, The Stanford Microarray
Database (SMD) has written a generic version of the GOTermFinder (as
originally seen on SGD -
http://genome-www4.stanford.edu/cgi-bin/SGD/GO/goTermFinder) that is
available as a set of object oriented Perl modules, and is distributed
under the MIT license, meaning you can do pretty much anything with it.

	GO::TermFinder will take a list of genes (any name that appears in
an annotation file will do, though there are caveats for ambiguous names),
an ontology file, and an annotation file, and determine the P_values for
the observed frequency of annotation to those genes for each GO node.
There are currently some differences between how the P-values are
calculated in our version with respect to SGD's version, in that we now
use the hypergeometric distibution, rather than the binomial, and we have
a multiple hypothesis testing correction algorithm (that in practice seems
to be roughly half-way between no correction, and BonFeronni), that should
minimize the number of false positives.  It doesn't currently include
SGD's wonderful graphic generation.

The code should shortly be available from the gmod site (www.gmod.org),
and I have also uploaded it to CPAN (see
http://search.cpan.org/author/SHERLOCK/).  This is the first time I've put
something on CPAN, so let me know if there's any glitches.  This initial
version has been fairly well tested, but the API's still need some work.
We would be happy to receive comments and criticism, and well as bug
reports and feature requests.  These can either be posted at the gmod
site, or mailed to me directly.  If you find it useful, it would also be
nice to know,

Cheers,
Gavin
___________________________________________________________

Gavin Sherlock
Dept. of Genetics
Center for Clinical Sciences Research
269 Campus Drive,
Room 2255b,
Stanford,
CA 94305-5166

Tel: 650 498 6012
Fax: 650 723 7016




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-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
========================================================================