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Re: Are DeprecatedClasses invisible to DIG Reasoners?

From: William Bug <William.Bug@drexelmed.edu>
Date: Mon, 20 Aug 2007 17:44:59 -0400
Message-Id: <015189DF-4E93-46D1-B633-3A2BD308719D@drexelmed.edu>
Cc: public-owl-dev@w3.org
To: "Ibach, Brandon L" <brandon.l.ibach@lmco.com>
Thanks, Brandon.

Yes - that makes the most sense, and as you say, is commensurate with  
the use of deprecation - as in Java - thus leaving it to an  
application to decide how to present this info to a user.  For  
instance, Protege adds a dark red "D" superscript to deprecated  
classes - just as information to the user.  This software development  
analogy is made in the OWL specs as well.

Now I more fully understand why the biomedical ontology community  
associated with the OBO Foundry and Gene Ontology are not using  
owl:DeprecatedClass.  They have the requirement of "retiring"/ 
deprecating a class when it was necessary to make changes that alter  
the semantic entailments of the class or its associated axioms.  The  
recommended practice is to clone the old class - giving it a new  
unique rdf:ID.  The older class is re-typed to a generic  
"_deprecated_class" and all its axioms are removed, so it will be  
opaque to reasoners - apart from the class axiom typing it as a  
"_deprecated_class".  The newly made clone then is used to make the  
changes that alter the underlying entailments associated with that  
class.

I was just trying to better understand how owl:DeprecatedClass  
relates to this practice.  The answer appears to be - it doesn't.

Thanks again.

Cheers,
Bill

On Aug 20, 2007, at 4:21 PM, Ibach, Brandon L wrote:

> Hi, Bill...
>     I also have little experience in interpreting these documents,  
> but I'll give it a shot.  I don't know what additional issues the  
> DIG protocol might bring into play, so I can only comment on the  
> OWL aspects.  It appears that you might be getting a little  
> confused between the semantics of a _class_ that is _typed_ as a  
> DeprecatedClass and the actual DeprecatedClass _axiom_, itself.  I  
> believe it is the axiom that "has no meaning in the model theoretic  
> semantics other than that given by the RDF(S) model theory",  
> meaning that an OWL reasoner should not treat the class any  
> differently than if it was not typed as a DeprecatedClass.
>     This interpretation of the statement you quoted from the OWL  
> Reference appears to be in line with the semantics you cited from  
> section 3.3 of the OWL Semantics document, wherein the presence of  
> a DeprecatedClass axiom only expands the extension of the rdf:type  
> relation and does not otherwise affect the semantics.
>     Given this, I believe you could say that DeprecatedClasses are  
> NOT invisible to reasoners, but that the DeprecatedClass axiom  
> (effectively) is.  (Mind you, I'd say this is true for OWL DL,  
> though not so much for OWL Full, about whose semantics I will not  
> claim any solid understanding.)  I believe this is in line with  
> most models for deprecation in computer languages.  That is,  
> something which is deprecated will continue to operate as it  
> always, but the user of it (be it a programmer, modeler, user,  
> etc.) may receive warning messages to remind them that they should  
> try to transition away from using it.
> -Brandon :)
>
>
>
> From: public-owl-dev-request@w3.org [mailto:public-owl-dev- 
> request@w3.org] On Behalf Of William Bug
> Sent: Saturday, August 18, 2007 5:33 PM
> To: public-owl-dev@w3.org
> Subject: Are DeprecatedClasses invisible to DIG Reasoners?
>
> Hi All,
>
> This is a naive question from someone who's never - in the context  
> of implementing a DIG Reasoner - had to interpret either the OWL  
> Direct Model-Theoretic Semantics:
> http://www.w3.org/TR/2004/REC-owl-semantics-20040210/ 
> direct.html#owl_DeprecatedClass_semantics
> or the OWL Abstract Syntax:
> http://www.w3.org/TR/2004/REC-owl-semantics-20040210/ 
> syntax.html#owl_DeprecatedClass_syntax_lite
> for owl:DeprecatedClass.
>
> I've read the W3C OWL docs - I've searched this lists archive -  
> I've read the SWOOP paper that talks a bit about versioning - and  
> I've Googled about, but nowhere can I find a simple answer to the  
> question:
>
> Are DeprecatedClasses invisible to DIG Reasoners?
>
> The following sentence in the OWL Language Reference implies they  
> might be:
>
> "(DeprecatedClass) has no meaning in the model theoretic semantics  
> other than that given by the RDF(S) model theory."
> http://www.w3.org/TR/2004/REC-owl-ref-20040210/#Deprecation
>
> I could write a simple OWL file with logical entailments from which  
> a reasoner can identify inferred sets, then go in and declare some  
> of the Classes as DeprecatedClasses to see how this effects the  
> reasoner output, but I thought I'd simply come to the source and  
> ask the experts.  Something tells me from the variety of scenarios  
> a reasoner might have to confront when parsing a complex OWL file  
> with specific Classes and/or Properties defined as deprecated that  
> the answer may not be straight-forward.
>
> Having said this, given in OWL DL, owl:Class is a direct subclass  
> of rdfs:Class (as opposed to being equivalent to rdfs:Class) and  
> owl:DeprecatedClass is also a direct subclass of rdfs:Class, it  
> seems reasonable to assume DeprecatedClasses definitions have not  
> logical entailments.
>
> What would it mean, then, for a Class definition to contain the  
> following type specification:
> <rdf:type rdf:resource="http://www.w3.org/2002/07/ 
> owl#DeprecatedClass"/>
> I've noticed when I specify an owl:Class as "Deprecated" in Protege- 
> OWL (<= v3.3beta), this element is added to the otherwise unchanged  
> class specification.
>
> Many thanks for any info or citations you can provide on this issue.
>
> Cheers
> Bill Bug
>
>
> 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 - William.Bug@DrexelMed.edu
>
>
>
>

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 - William.Bug@DrexelMed.edu
Received on Monday, 20 August 2007 21:45:13 GMT

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