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

[Gavin Sherlock]

Hi Hilmar,

	I would certainly like to get the TermFinder into BioPerl, and switch  
it to depend on some of the Ontology modules in BioPerl, rather than on  
the ones I wrote (though my modules have some functionality that I  
might need incorporated into the Ontology modules that exist already).   
I would be happy to maintain it, but my first question is : Is there a  
guide to getting new modules into BioPerl?  You mentioned that Ewan had  
written to the list about some minumum requirements, but the list  
didn't appear to searchable, so I couldn't find it,

Cheers,
Gavin

On Monday, March 24, 2003, at 12:24 PM, Hilmar Lapp wrote:

> 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
> -------------------------------------------------------------