[Bioperl-l] Bio::Ontology overhaul

[Paul Edlefsen]

Just FYI, I've made a Bio::SeqFeature::TypeI that ISA 
Bio::Ontology::TermI.  It provides methods for a tiny subset of ontology 
operations (just for searching the TypeI graph from a given TypeI 
starting point).  It is on the freaky dev branch.  It overloads 
stringification and is meant to generalize the Type stuff that Bio::Das 
already has.

:Paul

Ewan Birney wrote:

>>But - if the majority of people agrees with you, then the problem is
>>solved.
>>
>>Guys/gals on the list, please vote: ontology accessible from a term, or
>>the plain name of the ontology suffices?
>>
>>    
>>
>
>I am happy to go with hilmar's suggestion for the moment, and then if this
>causes hideous issues, back it out v. quickly.
>
>
>My sense is that down the 1.2 branch, ontologies will only be used in the
>context of biosql and probably well defined. On the main trunk however I
>think we have to embrace ontologies for seqfeature types (as the semantic
>win is so great... pardon the pun) which says that we should have
>developer releases (1.3 etc) and really pound on it...
>
>
>
>
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-- 
Paul T. Edlefsen  Software Engineer
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