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RE: BioPAX-discuss / "processing" RDF

From: Dan Kilburn <dkilburn@rcn.com>
Date: Tue, 10 Aug 2004 00:17:54 -0400
To: "'Internet Business Logic'" <ibl@snet.net>, <Eric.Neumann@aventis.com>
Cc: <public-semweb-lifesci@w3.org>, <ready2danceL@talkmatch.com>
Message-Id: <E1BuO5D-00027l-00@smtp01.mrf.mail.rcn.net>
Hi Eric and Adrian,


I have to weigh in on this one. I think what we're after here is a grammar
of biologically-relevant relationships that are at best imperfectly captured
in English, much as we may love our native tongue.  I for one mourn the
passage of Icarus, which allowed me move directly from RDF to a more
compelling visual representation of the data.  Without a tool similar to
Icarus, RDF leaves alot to be desired.






From: public-semweb-lifesci-request@w3.org
[mailto:public-semweb-lifesci-request@w3.org] On Behalf Of Internet Business
Sent: Monday, August 09, 2004 11:03 PM
To: Eric.Neumann@aventis.com
Cc: public-semweb-lifesci@w3.org
Subject: BioPAX-discuss / "processing" RDF


Hi Eric --

On Mon, 9 Aug 2004 11:07:55 you wrote...

'For those not comfortable in "processing" RDF (don't base your opinion on
trying reading RDF by eye), I suggest trying out JENA or CWM to see what is
possible in this space.'

Actually, even more is possible in this space.  A problem with RDF-based
inference is that it quickly becomes human-opaque, because the notation is
machine-oriented and the inferences are, well, intricate.

There's a demo called RDFQueryLangComparison1 that shows how to overcome
some of this difficulty.
One can run it by pointing a browser to the site listed below.  (The file
can also be downloaded from the link "Complete Examples")

The basic idea is to specify the inferences in rules that are close to
English (and open vocabulary).  Then, inferences that wind tortuously over
schema and base levels, use reification, etc, become clearer.  A plus is
that the representation shift allows the generation of step-by-step
English-like explanations of inference results.

HTH,    -- Adrian Walker

Internet Business Logic  --  online at www.reengineeringllc.com
Reengineering LLC,  PO Box 1412,  Bristol,  CT 06011-1412,  USA
Phone 860 583 9677     Mobile 860 830 2085     Fax 860 314 1029
Received on Tuesday, 10 August 2004 04:43:25 UTC

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