[Biojava-dev] BioJava compatibility with BioSQL-ORA?

[Len Trigg]

Michael Griffith <mg at guerrilla-tech.com> wrote:
> I am unclear after looking the current documentation and website if the
> classes in org.biojava.bio.seq.db.biosql.* are compatible with the
> BioSQL-Oracle implementation located at
> http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/sql/biosql-ora/?cvsroot=biosql.

As Mark replied, you'll need to get the bleeding edge version of
BioJava. That version supports the latest BioSQL schema, under MySQL,
PostgreSQL, HSQLDB, and Oracle.

I use Oracle with BioJava, however, when I first set it up I couldn't
get biosql-ora working, so I did a direct port of the MySQL schema. I
just had a look at the current biosql-ora and I think they should be
compatible.  Post if you have problems.

The current BioJava BioSQL binding departs somewhat in its ontology
handling (an extra table is required). If you don't use custom
ontologies you should be OK though.


Cheers,
Len.