[BioSQL-l] Description

[Paul Davis]

On 9/11/07, Chris Fields <cjfields at uiuc.edu> wrote:
> D'oh, it's in the README!
>
> ....
>
> This is the BioSQL distribution. BioSQL is a generic unifying schema
> for storing sequences from different sources, for instance Genbank or
> Swissprot.
>
> BioSQL is meant to be a common data storage layer supported by all the
> different Bio* projects, Bioperl, Biojava, Biopython, and Bioruby.
> Entries stored through an application written in, say, Bioperl could
> be retrieved by another written in Biojava.
>
> chris
>

I think this was the underlying idea behind standardizing the schema.
Granted I haven't groked all of the package's DB access layers, but
given what I've seen in the BioPython interface, I'm guessing this is
more of a theoretical possibility vs. a standard practice.

> On Sep 11, 2007, at 10:10 AM, Chris Fields wrote:
>
> > Here's a question I couldn't find the answer to: should any BioSQL-
> > loaded data (via BioJava, BioPerl, etc) be expected to fully round
> > trip across any BioSQL-utilizing language?  In other words, if I use
> > BioJava/Hibernate to load sequence data in to a BioSQL database and
> > use BioPerl to work with the data, can one expect it to work?
> >
> > My guess is no, as long as there is no formal specification...
> >
> > chris
> >
> > On Sep 11, 2007, at 9:54 AM, Richard Holland wrote:
> >
> >> -----BEGIN PGP SIGNED MESSAGE-----
> >> Hash: SHA1
> >>
> >> There is no formal specification for what goes where in BioSQL, but
> >> you
> >> can refer to the BioJava documentation for a good approximation of
> >> where
> >> a GenBank file should end up. The BioJava objects share similar
> >> names to
> >> the BioSQL tables and are mapped using Hibernate.
> >>
> >> The most useful parts of the docs are probably:
> >>
> >> http://biojava.org/wiki/BioJava:BioJavaXDocs#GenBank
> >>
> >> and:
> >>
> >> http://biojava.org/wiki/BioJava:BioJavaXDocs#Hibernate_object-
> >> relational_mappings.
> >>
> >> cheers,
> >> Richard
> >>
> >> Paul Davis wrote:
> >>> I've been going over the biosql schema and I was wondering if there
> >>> was a good place to read about examples of actual data that goes
> >>> into
> >>> each table. Specifically, I'm a bit confused about which parts of a
> >>> genbank record go in which tables.
> >>>
> >>> Thanks,
> >>> Paul Davis
> >>> _______________________________________________
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> >>>
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> >> _______________________________________________
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> >
> > Christopher Fields
> > Postdoctoral Researcher
> > Lab of Dr. Robert Switzer
> > Dept of Biochemistry
> > University of Illinois Urbana-Champaign
> >
> >
> >
> > _______________________________________________
> > BioSQL-l mailing list
> > BioSQL-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biosql-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
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