[Bioperl-l] Bio::Ontology additions

Allen Day allenday at ucla.edu
Fri Jun 20 12:37:20 EDT 2003


I just added a few new methods to the dagflat parser (for parsing dag-edit 
files).  The previous code had hardcoded the relationship types that were 
to be allowed (is_a, part_of, and a couple others).  I was trying to parse 
the cel ontology last night though, and couldn't because it had different 
terms (developsfrom).

So... I have added two new methods to SimpleGOEngine to accomodate this:

add_relationship_type( $type_name, $ontology)
	- adds new relationship types that don't already exist in the 
	ontology.  creates Bio::Ontology::RelationshipTypeI objects.
	returns 1 on successful creation, undef on failure.

get_relationship_type( $type_name)
	- returns the previously created Bio::Ontology::RelationshipTypeI
	object, or undef if there isn't one.

See the POD for full documentation.


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