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

[William Bug]

Thanks, Phil. This all makes perfect sense. Please see below for a brief clarification. Cheers, Bill On Sep 15, 2006, at 11:13 AM, Phillip Lord wrote: "WB" == William Bug <[EMAIL PROTECTED]> 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://www.w3.org/TR/2004/REC-owl-semantics-20040210/syntax.html#2).   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 www.neuroterrain.org 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 - [EMAIL PROTECTED] This email and any accompanying attachments are confidential. This information is intended solely for the use of the individual to whom it is addressed. Any review, disclosure, copying, distribution, or use of this email communication by others is strictly prohibited. If you are not the intended recipient please notify us immediately by returning this message to the sender and delete all copies. Thank you for your cooperation.