[Gmod-help] Apollo and Gbrowse Question

[Scott Cain]

Hi Martin,

The only documentation on the SeqFeature::Store database schema is
contained in the perl modules that interact with it.  Writing a
Java-based adaptor for it might prove difficult, as the main table
consists of serialized BioPerl SeqFeature objects.

If I may suggest: this seems like a lot of extra work, when a similar
system is already working with Apollo and GBrowse when using Chado as
the underlying database.  If you are concerned about performance when
using Chado as the database for GBrowse, you could implement a
procedure of periodically dumping GFF3 from Chado and automatically
loading it into a SeqFeature::Store database to power GBrowse.

Scott



On Wed, Nov 18, 2009 at 4:48 AM, info at martinkenner.net
<info at martinkenner.net> wrote:
>
> Dear gmod help
>
>
> I am working in a software project for the university of Freiburg, Germany.
> They want to use gbrowse in combination with Apollo.
>
> The gbrowse DB configuration is :
>
> db_adaptor    = Bio::DB::SeqFeature::Store
> db_args       = -adaptor DBI::mysql
>
> I am writing a adaptor for Apollo to get the selected data set from gbrowse
> and write back the modified or added data to the mysql DB.
>
> The questions for me now : Is there any documentation about the gbrowse
> SeqFeature DB structure ?
> Are there any information sources or existing activities about this ? ( I
> didn't find something )
>
>
> Thanks
>
> Martin Kenner
>
>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research