[Bioperl-l] ontology help

Marc Logghe Marc.Logghe at devgen.com
Sun Jun 27 10:08:57 EDT 2004

> I believe the current implementation of delegation from the 
> Bio::Ontology::Ontology methods to their counterparts in the 
> currently 
> used engine implementation expects that only terms and rel.ships from 
> the same ontology will be asked for.
> The original rationale behind this was to make it possible to use one 
> and the same engine instance to back multiple OntologyI instances. If 
> you did this, you would need to filter out terms from other 
> ontologies 
> co-using the engine instance.
> At hindsight I think this is probably over-engineered and trying to 
> solve a non-existing problem. So, we could as well demand that one 
> engine instance only serve one ontology instance and you're 
> on your own 
> if you do otherwise. This would then allow us to remove the 
> post-filtering code that filters hits returned from the engine.
> You could try and see whether that will solve your problem as well.
Thanks a lot for the help, Hilmar !!!!
At first, I indeed always used a separate engine. Taking your advice, a created a Bio::Ontology::Ontology first for the first ontology and reused that engine for the other two ontologies. And that did the trick !!!

Marc Logghe, Ph.D.
Senior Scientist
Scientific Computing Group
Devgen nv
Technologiepark 30
B - 9052 Ghent-Zwijnaarde
Tel: +32 9 324 24 83
Fax: +32 9 324 24 25

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