[Bioperl-l] OntologyTermI

[Ewan Birney]

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.