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<P><FONT SIZE=2>Hi Scott,<BR>
<BR>
Thanks a lot for your reply<BR>
<BR>
Inma<BR>
<BR>
-----Original Message-----<BR>
From: Scott Cain [<A HREF="mailto:cain.cshl@gmail.com">mailto:cain.cshl@gmail.com</A>]<BR>
Sent: Fri 8/8/2008 1:26 PM<BR>
To: Barrasa, Inmaculada<BR>
Cc: help@gmod.org<BR>
Subject: Re: [Gmod-help] gff database<BR>
<BR>
Hi Inma,<BR>
<BR>
The type=MyISAM tells MySQL what kind of table to create. I'm not a<BR>
MySQL person, but I believe MyISAM is the simple, no transaction, no<BR>
foreign key table that makes MySQL fast. Another option would be<BR>
INNODB (I think) which makes MySQL respect foreign keys and<BR>
transactions.<BR>
<BR>
That said, given what you want to do, I don't think you really want to<BR>
be mucking around with the schema by hand anyway. You might want to<BR>
think about using it via the BioPerl API and writing (fairly simple)<BR>
perl scripts to do the data manipulation if that is what you need to<BR>
do. Also, if you are working with reasonably recent WormBase GFF3,<BR>
you might want to look into using Bio::DB::SeqFeature::Store, which is<BR>
a newer database for GBrowse that works better with GFF3. It is<BR>
harder to manipulate in the database with direct SELECT statements,<BR>
but is much faster running GBrowse.<BR>
<BR>
(I just checked at WormBase still provides GFF2, so you can use that<BR>
with Bio::DB::GFF.)<BR>
<BR>
If you have more questions about implementation, you might want to<BR>
look at asking on the bioperl or GBrowse mailing lists:<BR>
<BR>
<A HREF="http://www.gmod.org/wiki/index.php/GBrowse">http://www.gmod.org/wiki/index.php/GBrowse</A><BR>
<BR>
<A HREF="http://bioperl.org/mailman/listinfo/bioperl-l">http://bioperl.org/mailman/listinfo/bioperl-l</A><BR>
<BR>
Scott<BR>
<BR>
<BR>
<BR>
On Fri, Aug 8, 2008 at 1:15 PM, Barrasa, Inmaculada<BR>
<Inmaculada.Barrasa@umassmed.edu> wrote:<BR>
> Great Thanks a lot, that' what I was looking for.<BR>
><BR>
> One more question, in the sub schema for mysql.pm at the end of the create<BR>
> table code there is code like: "type=MyISAM". What is that for?<BR>
><BR>
> For example:<BR>
> fgroup =>{<BR>
> table=> q{<BR>
> create table fgroup (<BR>
> gid int not null auto_increment,<BR>
> gclass varchar(100),<BR>
> gname varchar(100),<BR>
> primary key(gid),<BR>
> unique(gclass,gname)<BR>
> ) type=MyISAM<BR>
> }<BR>
> },<BR>
><BR>
> What is the code type=MyISAM for?<BR>
><BR>
> I am creating a database which will include the GFF tables so I can relate<BR>
> my data to the WormBase annotations and may be at some point have Gbrowser<BR>
> running locally too.<BR>
> I will only use the create code, not the type=MyISAM.<BR>
><BR>
><BR>
> Thanks again<BR>
><BR>
> Inma<BR>
><BR>
><BR>
> -----Original Message-----<BR>
> From: Scott Cain [<A HREF="mailto:cain.cshl@gmail.com">mailto:cain.cshl@gmail.com</A>]<BR>
> Sent: Fri 8/8/2008 12:39 PM<BR>
> To: Barrasa, Inmaculada<BR>
> Cc: help@gmod.org<BR>
> Subject: Re: [Gmod-help] gff database<BR>
><BR>
> Hello Inma,<BR>
><BR>
> I don't think the Bio::DB::GFF schema has changed much since 2002, so<BR>
> the current incarnation should be just fine. The schema itself is<BR>
> contained within the database adaptors for Bio::DB::GFF. For example,<BR>
> if you wanted the MySQL schema, you would have to look at the schema<BR>
> method of the Bio::DB::GFF::Adaptors::dbi::mysql. That module is<BR>
> contained in the BioPerl distribution, and the current version of that<BR>
> file can be browsed here:<BR>
><BR>
> <A HREF="http://code.open-bio.org/svnweb/index.cgi/bioperl/view/bioperl-live/trunk/Bio/DB/GFF/Adaptor/dbi/mysql.pm">http://code.open-bio.org/svnweb/index.cgi/bioperl/view/bioperl-live/trunk/Bio/DB/GFF/Adaptor/dbi/mysql.pm</A><BR>
><BR>
> Look for the line that starts "sub schema."<BR>
><BR>
> Scott<BR>
><BR>
><BR>
><BR>
><BR>
> On Fri, Aug 8, 2008 at 11:39 AM, Barrasa, Inmaculada<BR>
> <Inmaculada.Barrasa@umassmed.edu> wrote:<BR>
>><BR>
>> Hi,<BR>
>><BR>
>> Could you please tell me where I can find the sql statements to create the<BR>
>> gff tables?<BR>
>> I would like just to have the basic tables defined in 2002.<BR>
>><BR>
>> The Generic Genome Browser: A Building Block<BR>
>> for a Model Organism System Database<BR>
>> Lincoln D. Stein,1,5 Christopher Mungall,2 ShengQiang Shu,2 Michael<BR>
>> Caudy,3<BR>
>> Marco Mangone,1 Allen Day,1 Elizabeth Nickerson,1 Jason E. Stajich,4<BR>
>> Todd W. Harris,1 Adrian Arva,1 and Suzanna Lewis2<BR>
>><BR>
>><BR>
>><BR>
>> Thanks a lot your your help<BR>
>><BR>
>><BR>
>> Inma Barrasa<BR>
>><BR>
>><BR>
>> Walhout laboratory<BR>
><BR>
><BR>
><BR>
> --<BR>
> ------------------------------------------------------------------------<BR>
> Scott Cain, Ph. D. cain.cshl@gmail.com<BR>
> GMOD Coordinator (<A HREF="http://www.gmod.org/">http://www.gmod.org/</A>) 216-392-3087<BR>
> Cold Spring Harbor Laboratory<BR>
><BR>
><BR>
><BR>
<BR>
<BR>
<BR>
--<BR>
------------------------------------------------------------------------<BR>
Scott Cain, Ph. D. cain.cshl@gmail.com<BR>
GMOD Coordinator (<A HREF="http://www.gmod.org/">http://www.gmod.org/</A>) 216-392-3087<BR>
Cold Spring Harbor Laboratory<BR>
<BR>
<BR>
</FONT>
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