[Bioperl-l] Bio::Ontology

[Hilmar Lapp]

ChrisZ, Peter, and I sat over your proposal and brainstormed.

I'm trying to give a summary below. Chris, I think you've done a 
great job with your proposal, please don't take the following as an 
offense; it's just that we try to focus on a use case that is 
probably much too narrow for what you're doing. Who codes it wins 
the argument, so there are only winners here - 'cause all code :-)

So, generally speaking, what we were looking forward to here is one 
or very few dumbed-down interfaces, an implementation of which an 
ontology parser would return to you. We feel those interfaces should 
only contain the minimal set of methods you can't go without given 
straightforward use-cases. The implementation that the parser will 
return will often be much richer, but it doesn't have to be. I.e., 
it should be as painless as possible to implement those interfaces, 
but you can also be infinitely fancy in the implementation. We felt 
that your interfaces rather outlined all methods an implementation 
could possibly offer.

Also, we felt that your design wasn't very amenable to composition 
since the GraphVocabI inherits



On Thursday, September 19, 2002, at 01:45 PM, Chris Mungall wrote:

>
>
> 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)
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l@bioperl.org
>>> http://bioperl.org/mailman/listinfo/bioperl-l
>>>
>> --
>> -------------------------------------------------------------
>> Hilmar Lapp                            email: lapp at gnf.org
>> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
>> -------------------------------------------------------------
>>
>>
>
>
--
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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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