[Bioperl-l] Bio::Ontology

[Ewan Birney]

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.


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.



Any other thoughts?


AnnotableI might == Hilmar's Bio::Entry (or perhaps Bio::Entry is "just"
an AnnotableI)