[Biojava-l] BioJava, BioSQL versions

[Gang Wu]

Hi,

Just searched the archive and found the extra table term_relationship_term
as following. And then the demo code works. Should some lines be added in
the BioJava package document? There is no way for new BioJava developers to
use it witout explaining what's missing in the BioSQL schema. Thanks for the
helps from all of you.

==================================================================
CREATE TABLE term_relationship_term (
    term_relationship_id INTEGER NOT NULL,
    term_id INTEGER NOT NULL,
        PRIMARY KEY ( term_relationship_id, term_id ),
        UNIQUE ( term_relationship_id ),
        UNIQUE ( term_id ) );
==================================================================

Thanks,
Gang


-----Original Message-----
From: Len Trigg [mailto:len at reeltwo.com]
Sent: Wednesday, June 09, 2004 5:27 PM
To: gwu at molbio.mgh.harvard.edu
Cc: mark.schreiber at group.novartis.com; biojava-l at open-bio.org
Subject: Re: [Biojava-l] BioJava, BioSQL versions


"Gang Wu" <gwu at molbio.mgh.harvard.edu> wrote:
> I got the following exceptions:
> Exception in thread "main" org.biojava.bio.BioException: Error accessing
> ontologies
> Caused by: java.sql.SQLException: Base table or view not found,  message
> from server: "Table 'biosqldb.term_relationship_term' doesn't exist"

The BioJava Ontologies require an extra table in the schema, which
isn't part of the official BioSQL (this should *really* be resolved,
guys). A bit of searching on the archives will reveal more (I don't
recall the details myself).

It should also be possible to postpone creation of the core ontology
until it's actually needed, since many applications don't use it at
all (I've never used them).


Cheers,
Len.