[Bioperl-l] OntologyTermI

[Chris Mungall]

i'm just back from holiday and about to fly out to the Genome Informatics
meeting v shortly - i'll have something concrete to send out on wednesday.

do we have a set of use cases for this? i think this is important, before
we go diving in there.

i imagine most people want DAGs where all relationship types are
implicitly "is-a" or subclass/subsumption. GO style typed-relationship
DAGs where all relationship types are transitive and the 'true path' rule
holds would come next. to support this would be a straightforward port of
the current GO object model to bioperl, removing some of the clunkiness
and idiosyncracies along the way. however we may want to allow other kinds
of graph, eg cycles, non transitive relationship types, graphs where the
true path rule does not hold. this would require slightly more careful
design (please no escalating interfaces i don't think that's the right
way)

i do think the full frames-style ontologies with slots eg DAML+OIL is
outside the scope of bioperl and we shouldn't be focusing on these.

anyway, i'll have something more concrete when i reach cambridge.

On Mon, 2 Sep 2002, Ewan Birney wrote:

>
>
> On Sun, 1 Sep 2002, Chris Mungall wrote:
>
> > what about cyclical references? do we really want to go mucking around
> > with the WeakRef module?
> >
> > in the current GO object model, Terms are dumb, all the smarts are in the
> > graph object
> >
> > so you say
> >
> > $graph->get_children($term)
> >
> > rather than
> >
> > $term->children()
> >
> > which i prefer anyway
>
> This is pretty sensible. I guess this is now up to the implementors -
> Hilmar - if you or someone in your group wants to get stuck in there with
> "dumb" terms and ideally a Graph object, I think that would be great.
>
>
>
>