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OWL without RDF

From: William Bug <William.Bug@drexelmed.edu>
Date: Thu, 16 Nov 2006 13:43:08 -0500
To: systemsbiology hcls <public-semweb-lifesci@w3.org>
Message-Id: <492399DA-99CD-4049-8E5F-83AE41C68145@drexelmed.edu>
Hi All,

I wanted to give more "legs" to this discussion point that came up at  
the end of today's HCLSIG TCon, as I think it's extremely important  
for us users of RDF & OWL.

Sorry - I don't mean to be a "Chicken Little" on this issue - but as  
someone who needs to make practical technical recommendations to a  
large bioinformatics infrastructure project, this issue has me  
concerned.

Here is the link to the OWL ED 2006 manuscripts:

	http://owl-workshop.man.ac.uk/accepted06.shtml

I'd particularly recommend absorbing the details given in the  
following, as I believe these do an excellent job summarizing the  
justification being given by the developers of the OWL 1.1 spec for  
this move away from RDF:

	"Next Steps for OWL" (http://owl-workshop.man.ac.uk/acceptedLong/ 
submission_11.pdf)
	"Problems with OWL Syntax" (http://owl-workshop.man.ac.uk/ 
acceptedLong/submission_13.pdf)
	"Supporting Early Adoption of OWL 1.1 with Protege-OWL and FaCT+ 
+" (http://owl-workshop.man.ac.uk/acceptedLong/submission_15.pdf) -  
describes the new RDF-free version of ProtegeOWL with v1.1 support
	"The Manchester OWL Syntax" (http://owl-workshop.man.ac.uk/ 
acceptedLong/submission_9.pdf)
	"Putting OWL in Order: Patterns for Sequences in OWL" (http://owl- 
workshop.man.ac.uk/acceptedLong/submission_12.pdf)

These each present different aspects of the argument for moving ahead  
with OWL 1.1 independent of the requirement for the entirety of the  
normative spec to be expressible in RDF.

Just as a footnote, the DIG 2.0 API will include support for OWL 1.1  
operators:
	"Towards a Flexible Interface for Description Logic  
Reasoners" (http://owl-workshop.man.ac.uk/acceptedLong/submission_3.pdf)
	
As Eric pointed out, there has been considerable discussion of this  
move by members of the SemWeb community - e.g.:
	http://lists.mindswap.org/pipermail/owl/2005-December/000097.html
	http://www.mindswap.org/blog/2006/11/13/11-alternative/

There has also been some attempt by OWL developers to ease the  
transition:
	http://owl1_1.cs.manchester.ac.uk/rdf_mapping.html

As Eric said, some of the limitations, as opposed to be limits to the  
expressivity of RDF per se, are based on constraints imposed by RDFS  
and/or an RDF/XML representation - which as we all know is only ONE  
WAY of expressing RDF triplets.

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.

My understanding is some of these constraints (and other listed in  
the papers from the OWL ED meeting last week) are limited to RDFS,  
but I don't believe that is true of all of the constraints that - as  
they say - make some OWL 1.1 constructs inexpressible in RDF.  I'm  
far from an expert in the formal under-pinnings, however, so this is  
a question for the experts to answer.

I would add, the latter is one of the most valuable additions to the  
OWL 1.1 spec that runs right up against all the RDF/RDFS constraints  
imposed on annotations in OWL.  Those of us building ontologies in  
OWL & RDF recognize the need in the scientific domain to track  the  
"evidence" for any ontological assertion.  Many projects - SWAN & Bio- 
Zen are good examples - are very much ABOUT formally tracking data  
provenance and distilling it into evidence-supported ontological  
assertions.  I know from trying to use AnnotationProperties in the  
BIRNLex ontology, OWL 1.0 has very serious problems, when it comes to  
supporting the required links to "evidence".  The GO folks know this  
well, too, as "evidence codes" have always been at the heart of GO  
based annotations.  In fact, Chris Mungall and others have been  
working toward developing a more generic means of providing this  
capability to those both developing and using OBO Foundry-based  
ontologies.

Anyway - I think this is an important topic for us to consider - one  
for which - on this list - we have the ears of the experts - both in  
the design and use of OWL & RDF - who can help us all get a clearer  
sense of what the practical impact will be on our use of OWL & RDF.

I think Alan Ruttenberg and Jonathan Rees in particular - and many  
others I'm certain - have some insight to offer based on the work  
they've been doing.

Cheers,
Bill


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 Thursday, 16 November 2006 18:44:39 GMT

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