[Bioperl-l] Bio::Ontology

[Chris Mungall]

On Thu, 19 Sep 2002, Hilmar Lapp wrote:

> I agree, great stuff. It'd be even greater if you would have posted
> some thoughts earlier on. We have an almost working implementation
> ready to be committed too, ChrisZ posted some thoughts on that
> couple days ago. And of course it's not the same. That's actually
> exactly what I was trying to avoid.
>
> So I guess we will have two incompatible implementations in parallel
> for a while <sigh>

oops, sorry. have been incommunicado for much of the last 3 weeks (I did
mention this in the original thread i think).

> Also, our design has been much more bare-bones as that was all we
> needed.
>
> I'll have to look into chris' proposal in more detail.
>
> And actually I disagree that requiring to install Graph from CPAN
> would be bad. We're already requiring tons of dependencies to be
> installed, and many of them are a true pain in the ass on various
> platforms. Graph installed out-of-the-box on my machine (Mac OSX),
> there's no compiled code in it.

i think the important thing is to get our interface how we want it - then
we can plug in any implementation we like, from CPAN or from Bio::Graph

the CPAN graph module looks nice and comprehensive as far as most graph
theoretic operations are concerned. however, a graph and an ontology
aren't quite the same thing. for instance, the graph module doesn't treat
arc types as nodes in the graph itself, which can be useful.

I guess this points to another possibility - have a simple ontology object
model in bioperl, which covers the vast majority of use cases, and keep
the trickier ontology manipulation stuff in the GO codebase.

> 	-hilmar
>
> On Thursday, September 19, 2002, at 10:39 AM, 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.
> >
> >
> > 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)
> >
> >
> >
> >
> >
> >
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> >
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
>