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Re: Advancing translational research with the Semantic Web

From: Chris Mungall <cjm@fruitfly.org>
Date: Tue, 22 May 2007 08:29:23 -0700
Message-Id: <0248B2F9-12DE-424D-A29D-91093B714EB1@fruitfly.org>
Cc: Pat Hayes <phayes@ihmc.us>, Phillip Lord <phillip.lord@newcastle.ac.uk>, public-semweb-lifesci@w3.org
To: Marijke Keet <keet@inf.unibz.it>

On May 22, 2007, at 6:11 AM, Marijke Keet wrote:

>> <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.

Actually, I have to defend the OWL tools here, there are known  
problems with some of the relations in FMA and FMA-lite. These cause  
simple forward chaining reasoning to explode and I'm guessing the  
same thing happens with tableau algorithms.. the FMA developers are  
aware, these are being incrementally fixed in the main FMA and will  
hopefully all be fixed in the next release of FMA_lite in a month or so

The problems are of the sort

ALL rectum part_of male pelvis
ALL rectum part_of female pelvis

(but more widespread and deeper down the partonomy)

I'm guessing this is at least contributing to your problem

Thanks to Stuart Aitken for noticing this problem

> 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 15:31:20 UTC

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