[Bioperl-l] Fwd: [GMOD-devel] GO::TermFinder Announcement
Gavin Sherlock
sherlock at genome.stanford.edu
Thu Apr 3 09:15:08 EST 2003
Thanks Brian - I'll pay particular attention to the "Learn to read
documentation" section ;-). I did look around bioperl.org a little
though, and didn't see an obvious link,
Cheers,
Gavin
On Thursday, April 3, 2003, at 09:06 AM, Brian Osborne wrote:
> Gavin,
>
> Perhaps you're thinking of biodesign.pod?
>
> http://bioperl.org/Core/Latest/biodesign.html
>
> Brian O.
>
>
> -----Original Message-----
> From: bioperl-l-bounces at bioperl.org
> [mailto:bioperl-l-bounces at bioperl.org]On
> Behalf Of Gavin Sherlock
> Sent: Thursday, April 03, 2003 11:53 AM
> To: Hilmar Lapp
> Cc: lstein at cshl.org; bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] Fwd: [GMOD-devel] GO::TermFinder Announcement
>
> 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
>>> =====================================================================
>>> =
>>> ==
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at bioperl.org
>>> http://bioperl.org/mailman/listinfo/bioperl-l
>>>
>> --
>> -------------------------------------------------------------
>> Hilmar Lapp email: lapp at gnf.org
>> GNF, San Diego, Ca. 92121 phone: +1-858-812-1757
>> -------------------------------------------------------------
>
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