[Bioperl-l] OntologyTermI

[Hilmar Lapp]

Good comment Paul.

What I was actually trying to indicate with my response is that we could be going already in the absence of Graph::DAG, because it would rather narrow functionality, not widen or extend. I.e., if we assume that the ontologies we're going to work with already satisfy the acyclicy constraint, Graph::Directed would provide all we need. You'd need enforcement of the acyclicy constraint only for editing the ontology, and then only for adding/removing edges, not for editing the annotation of nodes.

That is, for the use cases that matter to us here, we're happy to use a Graph::DAG if someone writes it, but we don't need it to get going, unless I'm missing something. That's why it'd be interesting to know if someone did this exercise already.

	-hilmar

> -----Original Message-----
> From: Lincoln Stein [mailto:lstein@cshl.org]
> Sent: Monday, September 09, 2002 6:26 AM
> To: Hilmar Lapp
> Cc: Chris Mungall; Ewan Birney; Hilmar Lapp; Bioperl; Petre Dimitrov;
> Chris Zmasek
> Subject: Re: [Bioperl-l] OntologyTermI
> 
> 
> 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
>