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

[Hilmar Lapp]

I'm in email exchange with Gavin. Essentially Gavin needs to decide how  
much bioperl'ization would be needed and how much he is willing to do.  
I.e., he needs to say whether he wants this to move into bioperl. (it  
is going to need a maintainer, and there's not much doubt who would  
need to be that ...)

We need to check where his GO::AnnotationProvider fits in. I'm going to  
check this out, but others (Ewan, Aaron, Lincoln?) should do so too.  
Then there's some incompatibilities wrt how ontologies are read in and  
how the queries into an ontology are managed, but I suppose these can  
be worked out.

	-hilmar

On Monday, March 24, 2003, at 08:34  AM, Lincoln Stein wrote:

> 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
> ======================================================================= 
> =
>
>
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-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------