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

[Hilmar Lapp]

Naama -

it is the OntologyIO::obo parser that omits the typedefs. Parsing  
rather than skipping those could be added to the code; I also once  
started and almost completed a project to integrated the go-perl .obo  
parser into the Bio::OntologyIO framework, but the final touches fell  
victim to moving jobs and the ensuing upheaval.

If all you need to do is parsing a .obo-formatted ontology and  
traversing it in some way, go-perl might have all you need. If you  
need more than that, could you elaborate?

	-hilmar

On Mar 8, 2008, at 11:48 AM, Naama Menda wrote:

> Hi Hilmar,
>
> I have a loading script that uses Bio::Ontology::OntologyI  for  
> parsing  obo files and loading terms  into chado schema.
> I'm trying to find all relationship types, and it seems that the  
> parser looks at the distinct relationship types used by the terms  
> in the file,
> but not at the ' [Typedef] ' fields (I used 'get_predicate_terms()' ).
> This is important for storing the relationships in the right  
> context , for example all relationships types defined by Sequence  
> Ontology should be stored in
> the chado schema using the SO cv_id, while other relationship  
> types, not defined as Typedef in the obo file, should be stored  
> using the 'relationship' cv_id.
> Without a way to parse Typedefs, I also cannot use Bio::Ontology  
> for parsing OBO_REL file (http://www.obofoundry.org/ro/ro.obo).
>
> Is there another function in Bio::Ontology that handles Typedefs?  
> If not can one be added?
>
> Thanks!
> -Naama Menda

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