[Bioperl-l] Bio::Ontology additions

[Hilmar Lapp]

Allen could you add a test case (possibly with sample data?) that 
reveals the bug so that we can start fixing it.

	-hilmar

On Sunday, June 22, 2003, at 03:28  PM, Allen Day wrote:

> 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'...
>
> -allen
>
> 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 ...).
>>
>> 	-hilmar
>>
>
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-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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