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Re: Performance issues with OWL Reasoners => subclass vs instance-of

From: William Bug <William.Bug@DrexelMed.edu>
Date: Fri, 15 Sep 2006 12:09:41 -0400
Message-Id: <976D7D80-90B2-4470-A571-25B06EAF4E0C@DrexelMed.edu>
Cc: "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>, "chris mungall" <cjm@fruitfly.org>, <semantic-web@w3.org>, <public-semweb-lifesci@w3.org>
To: Phillip Lord <phillip.lord@newcastle.ac.uk>
Thanks, Phil.

This all makes perfect sense.

Please see below for a brief clarification.


On Sep 15, 2006, at 11:13 AM, Phillip Lord wrote:

>>>>>> "WB" == William Bug <William.Bug@DrexelMed.edu> writes:
>   WB> CLASSes represent UNIVERSALs or TYPEs.  The TBox is the set of
>   WB> CLASSes and the ASSERTIONs associated with CLASSes.
>   WB> INSTANCEs represent EXISTENTIALs or INDIVIDUALs instantiating a
>   WB> CLASS in the real world.  The ABox is the set of INSTANCEs and
>   WB> the ASSERTIONs associated with those INSTANCEs.
> I'd take a slight step back from this. You can think of classes and
> instances in this way. But in the OWL sense, a class is a logical
> construct with a set of computational properties. "Instances" is a
> more difficult term. OWL actually has individuals. The instance store
> uses "instances" because they are not really OWL individuals.
> There is also a philosophical concept of what a class is, what a
> universal is an so on, which may be somewhat different, and is also
> open to debate.

Admittedly, some of the issues addressed in discussions of biomedical  
ontology theory - especially those derived directly from formal Frege- 
style FOL expressions may not be supported in OWL.  What is supported  
in OWL are expressions one can construct in the specific DL OWL is  
based on, which I take it from what I've read on the OWL normative  
syntax page is roughly equivalent to SHIF(D) and SHION(D) (http:// 

>   WB> Properly specified CLASSes are defined in the context of the
>   WB> INSTANCEs whose PROPERTIES and RELATIONs they formally
>   WB> represent.
>   WB> Properly specified INSTANCEs are defined via their reference to
>   WB> an appropriate set of CLASSes.
> Think this would be circular. An OWL class is defined by the
> individuals that it might have in any model which fits the
> ontology. Not just the individuals it has an a specific model.

I didn't mean it as literally as it sounds - more in the sense of how  
you'd express this in Frege-style formalism:
	For the CLASS "mitochondrion", there exists some biomaterial entity  
for which all the assertions associated with the CLASS  
"mitochondrion" are true.

What this admittedly open ended definition allows is for the  
definition of CLASS "mitochondrion" to evolve as more detailed  
existential entities are described and new universal properties and  
relations for the CLASS "mitochondrion" are identified in the lab.

You are absolutely right, of course, in the case of OWL, to say a  
CLASS == {the set of all INDIVIDUALs who derive from that CLASS}  
would definitely be a circular definition that would likely confound  
a reasoner.

>   WB> Reasoners (RacerPro, Pellet, FACT++) generally have
>   WB> optimizations specific to either reasoning on the TBox or
>   WB> reasoning on the ABox, but it's difficult (i.e., no existing
>   WB> examples experts such as Phil and others can cite) to optimize
>   WB> both for reasoning on the TBox, the ABox AND - most importantly
>   WB> - TBox + ABox (across these sets).
> ABox is more complex than TBox, although I believe the difference is
> not that profound (ie they are both really complex). For a DL as
> expressive as that which OWL is based on, the complexities are always
> really bad. In other words, no reasoner can ever guarantee to scale
> well in all circumstances. This does not mean that you cannot build
> reasoners which will scale well in practice.
> Make sense?
> Phil

Bill Bug
Senior Research Analyst/Ontological Engineer

Laboratory for Bioimaging  & Anatomical Informatics
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA    19129
215 991 8430 (ph)
610 457 0443 (mobile)
215 843 9367 (fax)

Please Note: I now have a new email - William.Bug@DrexelMed.edu

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Received on Friday, 15 September 2006 16:43:44 UTC

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