[Bioperl-l] OntologyTermI

[Ewan Birney]

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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