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

[Naama Menda]

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