[Bioperl-l] Re: BioSQL or chado

Nathan (Nat) Goodman natg at shore.net
Wed Jul 30 08:40:03 EDT 2003

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).


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