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

[Allen Day]

> 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.

-Allen