[Biojava-l] OBDA and SeqDB

[Ewan Birney]

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.
> 
> 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.

OBDA has a CORBA binding which allows any BioJava compatible database to
be exposed to Perl and Python. Rather surprisingly it does actually work. 


The point about OBDA is that it is cross-language and standard. Therefore
"your own schema" can - by definition - fit into OBDA - however, you can
make your own BioJava bindings to your schema and then expose them as OBDA
compatible services either via CORBA or via the BioFetch system.





> 
> 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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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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