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Re: Advancing translational research with the Semantic Web

From: William Bug <William.Bug@DrexelMed.edu>
Date: Wed, 16 May 2007 07:48:42 -0400
Message-Id: <CE9FDF86-BDA6-479D-A01A-88723880C554@DrexelMed.edu>
Cc: Phillip Lord <phillip.lord@newcastle.ac.uk>, Eric Jain <Eric.Jain@isb-sib.ch>, Bijan Parsia <bparsia@cs.man.ac.uk>
To: public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>
On May 16, 2007, at 6:48 AM, Eric Jain wrote:

> Phillip Lord wrote:
>>>>>>> "EJ" == Eric Jain <Eric.Jain@isb-sib.ch> writes:
>>   EJ> Just catching up on reading papers :-)
>>   EJ> <http://www.biomedcentral.com/1471-2105/8/S3/S2>
>>   EJ> "It is also useful to know who believes something and
>>   EJ> why. However, there is no standard way of expressing such
>>   EJ> information about a statement [...]"
>>   EJ> Reification?
>> That's who, not why. The Gene Ontologies evidence codes are and
>> references are much closer. Also, I am not sure of the semantics  
>> of reification. Does it mean "I
>> made this statement", "I believe this statement" or "I am the person
>> responsible for the evidence on which this statement is based". All
>> three are independent I think.
> I assume what it means depends on the property that is used? In  
> place of (or in addition to) the popular dc:creator you could  
> introduce properties such as supportedBy, or whatnot. Arguably the  
> lack of established properties for such information may be a bit of  
> a problem, but the paper goes on to mention named graphs as a  
> possible solution, so that's not the level we're talking at. In any  
> case, no big deal, just another piece of evidence that reification  
> is an ugly neglected step-child :-)

Actually, DC provides several elements that could assist in providing  
greater subtlety to such reified expressions:
	dc:creator (as Eric points out)

The problem - as Bijan stated - is there is neither a standard syntax  
for expressing this subtlety - nor are there even sufficiently  
narrow, standard practices for what objects you link (i.e., the  
range) when using these specific dc elements.  In the end, to make  
use of these entities when expressing subtle provenance information,  
one would still need to embed a great deal of logic in your  
application to carry this burden - and that would be YOUR logic built  
on YOUR approach to representing this information, which, whether  
given by a formal syntax or not, others aren't likely to share.

OWL 1.1 does provide some help in this realm, as Bijan mentioned.  It  
is my understanding OWL 2.0 will provide even more.


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

Received on Wednesday, 16 May 2007 11:46:19 UTC

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