[Bioperl-l] Bio::Ontology::OntologyI

[Hilmar Lapp]

On Mar 9, 2008, at 9:34 PM, Naama Menda wrote:

> My main problem is that go-perl does not handle updates, so if I  
> want to update GO I need an empty schema. We find it more  
> complicated to re-load our annotations than to update cvterms and  
> their related data.
> Our loading script compares an existing load of an ontology to the  
> obo file and updates/insets/deletes accordingly.

load_ontology.pl in bioperl-db should have all this functionality,  
though of course that doesn't give you the typedef support (yet).

>
> We are now in the process of committing this code to GMOD

Cool - obviously load_ontology.pl doesn't work off of Chado but  
instead uses BioSQL as the schema (though the ontology model is  
*very* similar between the two).

BTW please keep the Bioperl list in the loop, others may have insight  
too or be interested in the information.

	-hilmar

-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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