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Re: Advancing translational research with the Semantic Web

From: Marijke Keet <keet@inf.unibz.it>
Date: Tue, 22 May 2007 15:11:50 +0200
Message-ID: <4652EC16.1090203@inf.unibz.it>
To: Pat Hayes <phayes@ihmc.us>
CC: Chris Mungall <cjm@fruitfly.org>, Phillip Lord <phillip.lord@newcastle.ac.uk>, public-semweb-lifesci@w3.org


>
> <snip>
>>>
>>> The history of computing is the history of "design patterns" at one 
>>> level that eventually get built into "higher level languages" at the 
>>> next level of abstraction up.
>>
>> I think I have a less optimistic view of progress in computer 
>> science. For example, many of the paradigmatic GoF design patterns 
>> are there to make up for deficiencies in the OO languages that 
>> *succeeded* more expressive and abstract functional languages.
>
> Amen to that. And we are living through an exactly similar transition 
> in representational languages, where DLs are re-inventing axioms of 
> classical logic.
it's not quite re-inventing, although it may be that "new features added 
to a language" are sometimes being sold as if they were novel. As for 
the n-aries in DLs (which are indeed trivial in CL), that is possible in 
DLs in theory for over 10 years and in software with iCOM for >7 years 
-- and do the automated reasoning over it, unlike with several other 
logics.

I like more expressivity as well, but then, I'm not implementing systems 
where I'd have to wait 'long' for query answers or see my computer hang 
upon classifying 1 instance in an 50-concept small ontology (with the 
latest pellet for owl 1.1). I did try to load in Protégé and SWOOP the 
FMA-lite, which is a 43MB OWL file. It failed. Reasoning over sections 
of the FMA that take into account only some constructors  is possible 
[1], which brings us back to your earlier comment that "people have 
argued against more expressive languages, in fact have argued with great 
force and vehemence,": if we have to chop up large ontologies anyway in 
order to be able to reason over them, we might as well do that in a 
structured manner with some simpler languages and (semi-)automated 
conversions for "dumbing down" a large and/or rich ontology to some 
slimmed version that is computationally tractable; that is, taking best 
of 'both worlds' with expressivity where desired/needed and performance 
where needed/desired.

[1] Zhang S, Bodenreider O, Golbreich C. Experience in reasoning with 
the Foundational Model of Anatomy in OWL-DL. In:Pacific Symposium on 
Biocomputing 2006, Altman RB, Dunker AK, Hunter L, Murray TA, Klein TE, 
(Eds.). World Scientific, 2006, 200-211. 
http://helix-web.stanford.edu/psb06/zhang_s.pdf

regards,
marijke

C. Maria Keet
KRDB Research Centre
Faculty of Computer Science
Free University of Bozen-Bolzano
Piazza Domenicani 3
39100 Bozen-Bolzano
Italy
tel: +39 04710 16128
fax: +39 04710 16009
email: keet@inf.unibz.it <mailto:keet@inf.unibz.it>
web: http://www.inf.unibz.it/krdb/
home: http://www.meteck.org <http://www.meteck.org/>
Received on Tuesday, 22 May 2007 13:12:00 UTC

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