[Gmod-help] gff database

[Barrasa, Inmaculada]

Hi Scott,

Thanks a lot for your reply

Inma

-----Original Message-----
From: Scott Cain [mailto:cain.cshl at gmail.com]
Sent: Fri 8/8/2008 1:26 PM
To: Barrasa, Inmaculada
Cc: help at gmod.org
Subject: Re: [Gmod-help] gff database
 
Hi Inma,

The type=MyISAM tells MySQL what kind of table to create.  I'm not a
MySQL person, but I believe MyISAM is the simple, no transaction, no
foreign key table that makes MySQL fast.  Another option would be
INNODB (I think) which makes MySQL respect foreign keys and
transactions.

That said, given what you want to do, I don't think you really want to
be mucking around with the schema by hand anyway.  You might want to
think about using it via the BioPerl API and writing (fairly simple)
perl scripts to do the data manipulation if that is what you need to
do.  Also, if you are working with reasonably recent WormBase GFF3,
you might want to look into using Bio::DB::SeqFeature::Store, which is
a newer database for GBrowse that works better with GFF3.  It is
harder to manipulate in the database with direct SELECT statements,
but is much faster running GBrowse.

(I just checked at WormBase still provides GFF2, so you can use that
with Bio::DB::GFF.)

If you have more questions about implementation, you might want to
look at asking on the bioperl or GBrowse mailing lists:

  http://www.gmod.org/wiki/index.php/GBrowse

  http://bioperl.org/mailman/listinfo/bioperl-l

Scott



On Fri, Aug 8, 2008 at 1:15 PM, Barrasa, Inmaculada
<Inmaculada.Barrasa at umassmed.edu> wrote:
> Great Thanks a lot, that' what I was looking for.
>
> One more question, in the sub schema for mysql.pm at the end of the create
> table code there is code like: "type=MyISAM". What is that for?
>
> For example:
>                 fgroup =>{
> table=> q{
> create table fgroup (
>     gid     int not null  auto_increment,
>     gclass  varchar(100),
>     gname   varchar(100),
>     primary key(gid),
>     unique(gclass,gname)
> ) type=MyISAM
> }
> },
>
> What is the code type=MyISAM for?
>
> I am creating a database which will include the GFF tables so I can relate
> my data to the WormBase annotations and may be at some point have Gbrowser
> running locally too.
> I will only use the create code, not the type=MyISAM.
>
>
> Thanks again
>
> Inma
>
>
> -----Original Message-----
> From: Scott Cain [mailto:cain.cshl at gmail.com]
> Sent: Fri 8/8/2008 12:39 PM
> To: Barrasa, Inmaculada
> Cc: help at gmod.org
> Subject: Re: [Gmod-help] gff database
>
> 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
>
>
>



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


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