[Bioperl-l] OntologyTermI

[Lincoln Stein]

In a classic "have your cake and eat it too" compromise, we could have a NodeI 
interface that Bio::Ontology::Term can choose to implement.  Methods are:

	children()		# return NodeI children
	parents()		# return NodeI parents
	all_children()	# return all NodeI children
	all_parents()	# return all NodeI parents

I still think it's a good idea for there to be a formal 
Bio::Ontology::Graph::Node that contains a term, but isn't the term itself.

Lincoln

On Thursday 29 August 2002 04:04 am, Ewan Birney wrote:
> On Wed, 28 Aug 2002, Matthew Pocock wrote:
> > Lincoln Stein wrote:
> > > 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.
> > >
> > > Lincoln
> >
> > Does the term /have/ any meaning outside of the graph? I guess any human
> > readable description has meaning outside the graph, but the whole point
> > of these formal graphical knowledge representations are to put all the
> > stuff we can pin down in the graph, not in the human readable text. Are
> > the graphs of terms definitely DAGs? I'm not convinced. That would
> > restrict the ontology to fairly booring relationships, unless I'm
> > missing something here. Perhaps you just mean a hierachial type system -
> > the subset or instanceof operator, not a full ontology.
>
> First question - yes - it does in a "lookup dictionary" way. Nowhere near
> the full richness of hte graph, but actually a very important role for
> ontologies.
>
>
> I am also going to stick my neck out here and claim that lots of
> useful ontologies will be either explicit DAGs or bigger graphs
> always used implicitly as DAGs and so DAG specific methods (all_parents,
> all_children) of a node will be very useful methods.
>
> > Matthew
> >
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-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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