[Open-bio-l] GAME -> BioSQL?

[David Huen]

On Friday 07 Jun 2002 7:59 pm, Hilmar Lapp wrote:
> I was actually asking about GAME because we are leaning towards
> converting every data source into GAME and then only loading GAME into
> our BioSQL build.
>
> Now your response prompts me to wonder whether I'm missing something.
> Would people think there is a better suited format or data-flow than
> going through GAME? (AGAVE? Not widely supported yet ...)
>
I think if you are going to consider GAME, you would really benefit from 
having a long talk with Chris Mungall at the Berkeley Drosophila Genome 
Project.  They are actively developing GAME as a means of distributing 
their genome annotation data.  They now have loaders that will load their 
versions of GAME into their Gadfly schema.  Gadfly itself and BioSQL may 
converge more and more with time.  I believe Chris will be at the Genome 
Bioinformatics meeting at Hinxton (I don't know where you are based).

He's your best bet as they are round-tripping to and from GAME now albeit in 
a somewhat different situation from yours.  A lot of their code is in Perl 
and I think they have GAME loaders in Java too for the Apollo tool.

If you can use their schema, they have most of the tools you are seeking 
already.  Of course, whether something tailored for Drosophila will suit 
your purposes enough remains to be seen.  It is also a work-in-progress and 
changes happen fairly frequently.

Regards,
David Huen