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Re: OWL without RDF

From: William Bug <William.Bug@DrexelMed.edu>
Date: Thu, 16 Nov 2006 20:57:10 -0500
Message-Id: <851953F2-B430-49E1-B714-DBBFEE26A79D@DrexelMed.edu>
Cc: Holger Knublauch <holger@topquadrant.com>, public-semweb-lifesci@w3.org
To: Jim Hendler <hendler@cs.umd.edu>
Dear Jim,

Many thanks.

This is all wonderful the hear.

If the person who's lab is responsible for developing and supporting  
one of the most widely used DIG reasoners says "these things are not  
mutually exclusive in any way", I've got much more confidence that  
all will be OK.  :-)

Does this mean these different formalisms will remain semantically  
interoperable?  That's really too general and vague a question to  
answer.  Let me try that again - Can we expect the assertions made in  
one of the more "lite" formalisms will be mappable into one of the  
more "heavy" formalisms in a lossless manner.  I assume going in the  
other direction, the translators must needs be lossy - at least for  
those ontological graphs making assertions or defining constraints  
not expressible in the more "lite" formalisms.  As I believe was  
stated on the public-owl-dev list, the hope would be any mappings  
would be able to at least avoid logical inconsistencies or  
contradictions.

Actually, all of that sounds very indefinite, now that I read it  
through again.  It's just going to take implementation of specific  
Use Cases to get a better understanding of what's possible - and  
practical.

It's also great to hear there will be support all around for  
ObjectProperties, given the critical role they play when trying to  
leverage the power of a reasoner to generate the inferred portion of  
your ontology.  As these ontologies of biomedical reality (e.g.,  
those associated with the OBO Foundry and other efforts across the  
globe) continue to grow in the attempt to provide more solid formal  
footing for detailed semantic descriptions of very complex biological  
data repositories, we absolutely must lean on the reasoners as much  
as is feasible as a tool to maintain ontological hygiene and to  
extend the leaves of the graphs we are creating to a level of  
granularity that keeps them relevant to researchers on the bleeding  
edge of their field.

The point you make regarding scalability in the integration space is  
also critical.  As you say, there has been discussion of this issue  
before on this list as a follow-up to last year's OWL ED 2005  
discussion/vetting of OWL Extensions, for instance.  There was  
another such discussion just a few weeks back following the HCLSIG  
F2F in Amsterdam, where again Scott Marshall and others made the  
point both within and across large-scale repositories, it can be more  
effective to consider a "lite" ontological approach, though the  
"heavier" more complete OWL-DL (and OWL 1.1) ontologies will  
definitely be a critical enabler, when one seeks to support more  
complex semantic queries in a complex space such as cross-species,  
multi-modality, multi-resolution studies of neurodegenerative disease  
as we are charged with in the BIRN project.

Thanks again for providing this very useful feedback.

Cheers,
Bill



On Nov 16, 2006, at 7:51 PM, Jim Hendler wrote:

> Bill - I think you see the key point - these things are not  
> mutually exclusive in any way - high end ontology use needs some of  
> the OWL 1.1 functionality, but wider adoption is likely to come in  
> the data integration space, where a lot can be done with the  
> simpler "OWL Mini" (or OWL Fast, or OWL Prime, or OWLET, or  
> whatever it might end up being called).
>  btw, the "?" marks in the graph didn't mean things were being left  
> out, it meant we weren't sure if including them would cause scaling  
> problems - I expect we will keep data and object type properties  
> because a lot of current tools support that distinction (for  
> example tools which turn OWL classes into web forms generally have  
> a different handling of each of these)
>  Work on this continues apace
>  JH
> p.s. There are some resource contention issues which I think are  
> relatively easily worked out, but there's also some difference in  
> the philosophy between the current OWL 1.1 people and the people I  
> mention working on the simpler OWL - but that's mostly because  
> we've been working in different spaces.
>
> At 7:31 PM -0500 11/16/06, William Bug wrote:
> Many thanks, Jim.
>
> I saw posts by you and others - as well as links to more detailed -  
> and very recent - discussions.
>
> These are all very helpful.
>
> I was particularly interested in the proposal you, Ora Lassilla,  
> and others have worked on to "absorb" much of the OWL Lite  
> constructs into RDF++ (I believe that is the name being used - two  
> proposals - the summary of which you give here - http:// 
> www.nabble.com/perspectives-on-OWL-v.next-and-RDF-tf2624829.html) -  
> minus many of the class axioms and Datatype Properties, but  
> including owl:disjointWith.
>
> I recall reading some on this in the past, but given these issues  
> related to OWL 1.1, those proposals take on a whole new semantic  
> value now - pun[ning] intended.      ;-)
>
> I also can definitely see the sense in the argument when trying to  
> determine where to go next, there is need to achieve a balance  
> between simplicity to catalyze wider adoption and the need to  
> provide new functionality to a subset of users.  I think its  
> actually a four way balance:
>         simplicity - robustness - performance/scalability -  
> expressivity
>
> These characteristics are not necessarily exclusive of - or the  
> inverse of - one another, though usually performance scales with  
> the inverse of expressivity, at least when comparing across very  
> large differences in expressivity.
>
> The position you choose to target in this space really depends on  
> what you are trying to achieve, obviously.
>
> Cheers,
> Bill
>
>
> On Nov 16, 2006, at 3:01 PM, Jim Hendler wrote:
>
> actually, we're trying to move the discussion to public-owl-dev@w3.org
> there's a thread there that expresses some of my concerns about  
> moving away from the OWL syntax - given that the primary tools out  
> there right now still assume the OWL is integrated with the RDF  
> graph...
>
> At 2:52 PM -0500 11/16/06, William Bug wrote:
> As I expected, the experts are listening.  :-)
>
> Many thanks, Holger.  That's extremely important to know.
>
> I will dig into the thread for more detail.  One main concern would  
> be whether that was just a token gesture to stay compatible for  
> now, as opposed to a commitment to remain compatible, until or  
> unless an effective alternative is provided to representing very  
> large knowledgebases in RDF.
>
> I think more than anything I was a bit overwhelmed by the  
> collective picture given by those half-dozen or so presentations  
> from last week's meeting.  The meeting seemed "fresh" enough, so  
> that it could be expected to be reflective of the status quo.  I  
> assume there was much heated discussion during the meeting, that  
> would have filled out such detail - or such has been carried out on  
> the owl-dev list.
>
> I suppose it's also a good idea to dig into the OWL Extensions list  
> hosted by Jim Hendler's lab:
>                 http://lists.mindswap.org/mailman/listinfo/owl
>
> Cheers,
> Bill
>
>
> On Nov 16, 2006, at 2:33 PM, Holger Knublauch wrote:
>
>
> However, I'd point out, in the last document, where they describe a  
> mapping of OWL 1.1 to RDF, they make the following caveat:
> Not every OWL 1.1 ontology can be serialized in RDF. In particular,  
> ontologies using the following features of OWL 1.1 cannot be  
> serialized:
>    1. punning and
>    2. annotations on axioms.
>
> Please see a recent thread on the public-owl-dev mailing list about  
> this: http://www.nabble.com/Limitations-of-OWL-1.1-to-RDF-mapping- 
> tf2639224.html
>
> Bijan states:
> "The RDF mapping has lagged behind the others, but the plan is to
> extend the mapping to cover these cases."
>
> Holger
> TopQuadrant, Inc.
> http://www.topbraidcomposer.com
> http://composing-the-semantic-web.blogspot.com/
>
>
> 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
>
>
> --
> Prof James  
> Hendler                                                       
> hendler@cs.umd.edu
> Dept of Computer Science                                       
> http://www.cs.umd.edu/~hendler
> AV Williams Bldg                                                   
> 301-405-2696 (work)
> Univ of  
> Maryland                                                      
> 301-405-6707 (Fax)
> College Park, MD 20853 USA
>
>
> 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
>
>
> -- 
> Prof James Hendler                              hendler@cs.umd.edu
> Dept of Computer Science                      http://www.cs.umd.edu/ 
> ~hendler
> AV Williams Bldg                          301-405-2696 (work)
> Univ of Maryland                             301-405-6707 (Fax)
> College Park, MD 20853 USA
>

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 Friday, 17 November 2006 01:58:40 GMT

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