[Bioperl-l] OntologyTermI

[Chris Mungall]

I like this

however, as Bio::Ontology::Graph is likely to be a completely generic
graph module, why not just use the namespace Graph:: and have it as a
seperate CPAN module (but possibly keeping the cvs in bioperl-live)? just
a thought.

once you seperate term from node, do you really need a node object? why
not just have a graph object and treat the nodes and relationship types as
strings (possibly namespaced, but the graph module doesn't care about
this).

On Thu, 29 Aug 2002, Ewan Birney wrote:

> On Wed, 28 Aug 2002, Lincoln Stein wrote:
>
> > I believe that the idea of the term should be separated from the idea of a
> > graph of terms.  I think also that the idea of an association between a term
> > and a set of biological objects should also be separate.
> >
> > I'd propose something like this:
> >
> > 	Bio::Ontology::TermI;   # why repeat the word Ontology?
> >
> >
> > 		Encapsulates the term ID, the term name, the term definition, the term
> > 		aliases,and possibly the "obsolete" tag.
> >
> > 	Bio::Ontology::Graph::NodeI;
> >
> > 		A node in a graph.
> >
> > 	Bio::::Ontology::Graph::DAGI;
> >
> > 		Encapsulates the graph traversal methods.
> >
> > 	Bio::Ontology::Term::AssociationI;
> >
> > 		Maps a term to a set of biological objects.
> >
> > The nice thing about separating the Term from the DAG is that you can then
> > reuse the same term in different types of graphs, or chuck the graph entirely
> > without scrambling the meaning of the term.
>
> I am with Lincoln here. This would be the set up I would use as well.
>
>
>
>