[Bioperl-l] Bio::Ontology

[Chris Mungall]

On Thu, 19 Sep 2002, Ewan Birney wrote:

>
> This is awesome stuff Chris, and as you know I like the basic layout. I
> feel that it is better to have Bio::Graph "inside" Bioperl - I know there
> is a nasty catch-22 here (surely it is generic...) but if we make this a
> hard dependancy --- which I would really like, making sure each sequence
> feature gets automagically attached to a Sequence Ontology term --- then
> asking people to install a separate graph package to get embl parsing to
> work is BAD.

Yup, I agree

Since we spoke at Hinxton I've moved the graph stuff to Bio::Graph

the stuff in Bio::Ontology depends on Bio::Graph but not vice versa

The graph interface does extend from the TripleStore interface, which is
part of the Bio::Graph namespace

> I also think that although graphs are seemingly generic, the use of graph
> structures end up being specialised, so the methods (eg, subsumed and
> inherieted) become more specific than people think.

hmm, not sure what you mean

but I think that it's a good thing that arcs / relationships between terms
such as subsumes/inherits are both specific and well-defined.

> Any other thoughts?
>
>
> AnnotableI might == Hilmar's Bio::Entry (or perhaps Bio::Entry is "just"
> an AnnotableI)

i'd be happy to make Bio::Entry the thing that is annotated; I'll wait and
see how this pans out. This part isn't necessary for using the
Bio::Ontology classes for seqfeature types.