[Gmod-help] gff database

[Scott Cain]

Hello Inma,

I don't think the Bio::DB::GFF schema has changed much since 2002, so
the current incarnation should be just fine.  The schema itself is
contained within the database adaptors for Bio::DB::GFF.  For example,
if you wanted the MySQL schema, you would have to look at the schema
method of the Bio::DB::GFF::Adaptors::dbi::mysql.  That module is
contained in the BioPerl distribution, and the current version of that
file can be browsed here:

http://code.open-bio.org/svnweb/index.cgi/bioperl/view/bioperl-live/trunk/Bio/DB/GFF/Adaptor/dbi/mysql.pm

Look for the line that starts "sub schema."

Scott




On Fri, Aug 8, 2008 at 11:39 AM, Barrasa, Inmaculada
<Inmaculada.Barrasa at umassmed.edu> wrote:
>
> Hi,
>
> Could you please tell me where I can find the sql statements to create the
> gff tables?
> I would like just to have the basic tables defined in 2002.
>
> The Generic Genome Browser: A Building Block
> for a Model Organism System Database
> Lincoln D. Stein,1,5 Christopher Mungall,2 ShengQiang Shu,2 Michael Caudy,3
> Marco Mangone,1 Allen Day,1 Elizabeth Nickerson,1 Jason E. Stajich,4
> Todd W. Harris,1 Adrian Arva,1 and Suzanna Lewis2
>
>
>
> Thanks a lot your your help
>
>
> Inma Barrasa
>
>
> Walhout laboratory



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D. cain.cshl at gmail.com
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory