[Bioperl-l] Bio::Ontology additions
allenday at ucla.edu
Sat Jun 21 23:28:23 EDT 2003
done. btw, i've introduced a bug in the parsing of secondary term
relationships when they use custom predicates. from what i've seen this
doesn't affect the graph structure as the secondary relationships are
redundant, but it still needs fixin'...
On Sat, 21 Jun 2003, Hilmar Lapp wrote:
> On Friday, June 20, 2003, at 11:37 AM, Allen Day wrote:
> > 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.
> It sounds like these could be generally useful (or even required). If
> so you may want to consider adding them to OntologyEngineI; generally
> speaking the parser may be supplied with an engine implementation
> different from SimpleGOEngine (although I believe right now the parser
> will throw up for other reasons if you do that ...).
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