[Bioperl-l] Bio::Ontology

[Hilmar Lapp]

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>

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.

	-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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--
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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