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Re: Advancing translational research with the Semantic Web

From: Pat Hayes <phayes@ihmc.us>
Date: Wed, 23 May 2007 08:53:31 -0700
Message-Id: <p06230948c27a129f5448@[]>
To: Marijke Keet <keet@inf.unibz.it>
Cc: Chris Mungall <cjm@fruitfly.org>, Phillip Lord <phillip.lord@newcastle.ac.uk>, public-semweb-lifesci@w3.org

>>>>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 
>>>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.

I think it is often re-inventing. Take the 
current fuss about a W3C rule language, and how 
to 'add' it to OWL. Both rules and OWL are easily 
defined subsets of full FOL, so this ought to be 
close to trivial. BUt this isn't how it is being 
treated, and it is turning out to be anything but 
trivial, and is widely stated to require new, 
original research.

>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 
>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 

I agree, of course there is an 
expressivity/efficiency trade-off. And in many 
ways, DLs have identified an important 'sweet 
spot' between the extremes. But the main role of 
a Web logic is to be a semantically clear, 
coherent, interchange medium. An expressive logic 
with a sound semantics is the best choice for 
that; and the various (because there are more 
than one) tractable subsets of it can be treated 
by efficient reasoners. The problem with the 
current SWeb design is that a variety of 
'simpler' (actually the less expressive languages 
are often syntactically more complex) languages 
is still a VARIETY, which wrecks information 

Pat Hayes

>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. 
>C. Maria Keet
>KRDB Research Centre
>Faculty of Computer Science
>Free University of Bozen-Bolzano
>Piazza Domenicani 3
>39100 Bozen-Bolzano
>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/>

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Received on Wednesday, 23 May 2007 15:53:51 UTC

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