[Obo-discuss] Storing obo ontologies in an RDBMS

[Arne M. <arn...@gm...>]

Dear All,

we've created some customized ontologies (pathology and anatomy) in obo
format (created with a modified version of oboedit2 that helps converting
our legacy and semi-controlled internal vocabulary into a "proper"
ontology).

I'd like to store these ontologies in a database and to make it accessible
to our bioinformatics people (incl. myself) to include it in a range of
datamining applications.

What would be the best strategy for storage and querying?

- RDF triple store with a custom api on top (java/perl)
- develop my own SQL schema based on e.g. the Gene Ontology schema + custom
api in java/perl
- using OBD (and maybe a simple constom api on top of the obd api)

I'd be happy to discuss your experience with storing/querying/mining obo
ontologies. In particular, has anybody experience with OBD, i.e. loading an
obo file into  the obd schema an then using the api to query it - how mature
is obd?

   thanks a lot for discussion
   +regards,

   Arne