[Gmod-schema] RE: [Bioperl-l] Re: BioSQL or chado

[Arnaud Kerhornou]

Hi Hilmar

As Chris mentioned I'm investigating how feasible it would be to bind 
Bioperl and GUS using the Bioperl-db interfaces implementation.
Could you sent me the slides from your talk at the BOSC as well ? I 
think they will be handy.

Thanks
Arnaud

Chris Stoeckert wrote:

> Hi Nat,
> Coming into this exchange late but just wanted to mention our plans 
> for  BioPerl and GUS. GUS has its own object layer but we are 
> exploring  BioPerl for transferring standard sequence analyses into 
> the GUS  tables. Arnaud Kerhornou (GeneDB) at the Sanger Institute is 
> working on  this.
>
> Cheers,
> Chris
>
> On Wednesday, July 30, 2003, at 08:40  AM, Nathan ((Nat)) Goodman wrote:
>
>> Thanks, everyone, for the helpful comments!
>>
>> Hilmar wrote:
>>
>>> I gave an extensive talk at BOSC03 on biosql and bioperl-db, and I can
>>> email you the slides if you are interested.
>>
>>
>> Yes, the slides would be great!  I'm starting to feel my way through  
>> the
>> code.  I gather that to make class XXX persistent, I create a
>> Bio::DB::BioSQL::XXXAdapter class, yes?  Seems simple enough...  
>> (famous last
>> words :)
>>
>> I should have made my needs a bit more clear.  I want to use existing
>> schemas and adapters for existing BioPerl classes.  I accept the
>> responsibility to create schemas and adapters for new BioPerl (or  
>> BioPerl
>> wannabe) classes I write, and hope that others will do the same for  
>> BioPerl
>> classes they write. I expect to access the database through BioPerl  
>> only
>> (except for occasional admin purposes) which means that the only  
>> features
>> I'll ever use are ones that are visitble through BioPerl.
>>
>> I'm trying to hitch my wagon to the schema that has the most mature  
>> BioPerl
>> binding and that is likely to be most widely adopted by the 
>> community  of
>> BioPerl developers (so that the BioPerl binding will continue to  
>> improve).
>>
>> Thanks,
>> Nat
>>