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

[Chris Mungall]

On Tue, 29 Jul 2003, Allen Day wrote:

> > BioSQL certainly has the tightest integration with bioperl (and the other
> > bio* projects). This is through an O/R layer.
> >
> > chado has no direct integration with bioperl. I don't think there is any
> > O/R layer or OO API planned (although some biojava folks have expressed an
> > interest in this), Scott Cain has written a chado adapter for gbrowse
> > (which uses bioperl objects) which could be extracted to form an API in
> > its own right (although it is currently limited to the kind of API
> > calls you need to make a genome viewer).
> >
> > Many of the chado developers favour XML over objects. Chado-XML DTD is
> > derived directly from the relational schema. The chado developers at
> > Harvard have written a generic XML<->DB tool, which can be used in place
> > of an API or O/R mapping. Of course, we still want to be able to use
> > bioperl objects, so there are Bio::SeqIO::chadoxml classes being
> > developed. The most likely route will be DB<->ChadoXML<->bioperl.
>
> There is a perl O/R layer for chado -- it's autogenerated Class::DBI code
> from the CREATE TABLE statements.  There are not yet any adapters written
> that convert the Class::DBI objects to/from bioperl objects.

Yes of course, sorry, totally spaced on this part, I've been focused on
the components developed by the harvard/flybase folks.

Is there any plans to write the bioperl bridge anytime soon?

> -Allen
>
>