[Bioperl-l] Bio::Ontology overhaul

[Aaron J Mackey]

On Wed, 26 Feb 2003, Hilmar Lapp wrote:

> Guys/gals on the list, please vote: ontology accessible from a term, or
> the plain name of the ontology suffices?

I'd guess that many people (read: me and others like me) will be first
approaching ontologies via seqfeature-associated terms, and would then
like to get at related terms.

Can I get an OntologyTermI without having first made an OntologyI and
OntologyEngineI?

(why is it an engine and not an OntologyTerm factory?  I guess the
OntologyEngineI could be given an OntologyFactoryI to produce the
OntologyTermI's it needed ... All this pattern-speak gets very confusing).

Does accessing an OntologyTermI via a seqfeature (or some other
OntologyTerm-associated container with a $term = $obj->term functionality)
auto-instantiate the OntologyI "namespace" of the term, which then creates
an OntologyEngineI to build the OntologyTermI that was requested (thus
setting up the circular reference)?

If so, how could an OntologyEngineI object manage to be reused for another
OntologyTermI that lived in a different OntologyI?

Or do I (the lowly biologist trying to program with BioPerl), need to
instantiate my own OntologyEngineI (and/or OntologyI) before getting at
OntologyTermI's?

-Aaron

-- 
 Aaron J Mackey
 Pearson Laboratory
 University of Virginia
 (434) 924-2821
 amackey at virginia.edu