[Biojava-l] OBDA and SeqDB

[Jason Stajich]

On Mon, 8 Apr 2002, Schreiber, Mark wrote:

> Hi -
>
> So is there a plan to do a OBDASeqDB which would act like the BioSQLDB
> in biojava but not require the underlying SQL schema.
>

In Bioperl we have the Bio::DB::RandomAccessI interface which all the OBDA
clients implement allowing us to treat data from all OBDA providers
generically.  This has two methods get_Seq_by_acc and get_Seq_by_id (to
handle the case when a provider has data indexed in different ways).
This method returns a Bio::SeqI object and this allows all of the OBDA
providers to implement this interface.  BioJava should already have that
interface in SeqDB I believe so that is where you should start.

However, please understand that the point of the OBDA is to be able to
reuse the same data provider across all the OBF projects, so you data
won't really be OBDA compliant since none of the other toolkits will know
how to read from that schema.

> Does OBDA actually place restrictions on the underlying schema? The
> reason I ask is that our in house database doesn't match the BioSQL
> schema closely enough for it to be useful but it would be nice to use
> things developed in OBDA if we can.
>

Yes in the sense that it has be readable by all the other projects.  If
you only want to provide Java access to your data then you just need to
implement the BioJava SeqDB interface and you're done.

You could experiment with migrating to the BioSQL schema by building
in-memory biojava objects from your db and then write these objects into
db with the biosql schema and voila, you've done a data transform from
your schema to biosql - if you run your code on both schemas and get
different answers you have an incompatibility...

> Mark
>
> > -----Original Message-----
> > From: Jason Stajich [mailto:jason@cgt.mc.duke.edu]
> > Sent: Monday, 8 April 2002 10:31 a.m.
> > To: Schreiber, Mark
> > Cc: Keith James; BioJava List
> > Subject: RE: [Biojava-l] FeatureHolder.containsFeature()
> >
> >
> > On Mon, 8 Apr 2002, Schreiber, Mark wrote:
> >
> > > Actually can some one inform me of the difference between
> > the BioSQL
> > > and the Open Bioinformatics Database Specification??
> > >
> > > Mark
> >
> > BioSQL is a subset of OBDA - OBDA includes standards for
> > sequence retrieval from HTTP, local Flat files (Berkeley DB
> > indexed and a new index format), BioCORBA, and BioSQL.
> >
> > If you have specific gripes or kudos for OBDA we should move
> > them over to open-bio-l@open-bio.org to try and be
> > cross-project friendly.
> >
> > We hope to have a full fledged standard proposal put together
> > in the next few months, right now most things are split up in
> > different working docs - all available from the obf-common
> > CVS repository - see http://cvs.open-bio.org for info on downloading.
> >
> > HTH.
> >
> > -j
> >
> > --
> > Jason Stajich
> > Duke University
> > jason@cgt.mc.duke.edu
> >
> >
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-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu