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

[SLetovsky at aol.com]

In a message dated 7/29/2003 11:54:06 PM Eastern Standard Time, 
allenday at ucla.edu writes:

> >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.
> 
> 

Peili Zhang at FlyBase Harvard, who is currently vacationing in the French 
countryside,
has developed a BioPerl<->chadoXML module. It is not 100% complete -- there
were some issues about how to map to less expressive formalisms such
as GenBank. If anyone is interested in details I suggest they contact her in 
2 weeks.

Cheers, -Stan