[Bioperl-l] Bio::Ontology overhaul

[Hilmar Lapp]

You cc'ed ChrisM, so I guess you know that ChrisM did something similar 
in Singapore? Chris, did you commit that to the 'freaky' branch, or did 
you open your own branch, or is it on the main trunk?

	-hilmar

On Thursday, February 27, 2003, at 10:29  AM, Paul Edlefsen wrote:

> 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
> <<<<<<<<<<<<<<<<  >>>>>>>>>>>>>>>>>
> The Institute for Systems Biology
> 1441 North 34th Street
> Seattle, Washington 98103-8904
> <<<<<<<<<<<<<<<<  >>>>>>>>>>>>>>>>>
> Email: paul at systemsbiology.org
> Phone: (206)732-1336
> Fax:   (206)732-1260
>
>
>
>
>
-- 
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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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