[Bioperl-l] OntologyTermI

[Lincoln Stein]

This sounds right.  Is cycle checking computationally expensive?

Lincoln

On Tuesday 03 September 2002 08:47 pm, Hilmar Lapp wrote:
> Essentially Graph::DAG would override $G->add_cycle() to throw an
> exception, and add checks such that $G->add_edge() can't introduce a
> cycle? Would it need more than that?
>
> Has anyone gone through the exercise of putting e.g. GO into a
> Graph::Directed object?
>
> 	-hilmar
>
> On Tuesday, September 3, 2002, at 04:44  PM, Lincoln Stein wrote:
> > That's certainly a possibility.  The Graph::* namespace on CPAN has
> > room for a
> > DAG.  Presumably it would inherit from Graph::Directed.
> >
> > Lincoln
> >
> > Module          Graph           (J/JH/JHI/Graph-0.201.tar.gz)
> > Module          Graph::BFS      (J/JH/JHI/Graph-0.201.tar.gz)
> > Module          Graph::Base     (J/JH/JHI/Graph-0.201.tar.gz)
> > Module          Graph::DFS      (J/JH/JHI/Graph-0.201.tar.gz)
> > Module          Graph::Directed (J/JH/JHI/Graph-0.201.tar.gz)
> > Module          Graph::HeapElem (J/JH/JHI/Graph-0.201.tar.gz)
> > Module          Graph::Kruskal  (S/ST/STBEY/Graph-Kruskal-2.0.tar.gz)
> > Module          Graph::Reader   (N/NE/NEILB/Graph-
> > ReadWrite-1.07.tar.gz)
> > Module          Graph::Reader::Dot (N/NE/NEILB/Graph-
> > ReadWrite-1.07.tar.gz)
> > Module          Graph::Reader::HTK (N/NE/NEILB/Graph-
> > ReadWrite-1.07.tar.gz)
> > Module          Graph::Reader::XML (N/NE/NEILB/Graph-
> > ReadWrite-1.07.tar.gz)
> > Module          Graph::Traversal (J/JH/JHI/Graph-0.201.tar.gz)
> > Module          Graph::Undirected (J/JH/JHI/Graph-0.201.tar.gz)
> > Module          Graph::Vertex   (J/JH/JHI/Graph-0.005.tar.gz)
> >
> > On Monday 02 September 2002 12:43 am, Chris Mungall wrote:
> >> 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.
> >
> > --
> > ========================================================================
> > Lincoln D. Stein                           Cold Spring Harbor
> > Laboratory
> > lstein@cshl.org			                  Cold Spring Harbor, NY
> > ========================================================================

-- 
Lincoln Stein
lstein@cshl.org