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:[EMAIL PROTECTED]] > > 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 [EMAIL PROTECTED] 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 > > [EMAIL PROTECTED] > > > > > ======================================================================= > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > ----------------------------------------------------------------- Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420 <[EMAIL PROTECTED]>. ----------------------------------------------------------------- _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
