[Bioperl-l] Bio::Ontology overhaul

[Chris Mungall]

I did it on the collections branch

On Thu, 27 Feb 2003, Hilmar Lapp wrote:

> 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
> >
> >
> >
> >
> >
>