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Re: BioPAX-discuss / "processing" RDF

From: Matt Halstead <matt.halstead@auckland.ac.nz>
Date: Tue, 10 Aug 2004 17:10:29 +1200
Message-Id: <98E98776-EA8B-11D8-9F97-000A95B32AC4@auckland.ac.nz>
Cc: <Eric.Neumann@aventis.com>, <public-semweb-lifesci@w3.org>, "'Internet Business Logic'" <ibl@snet.net>, <ready2danceL@talkmatch.com>
To: "Dan Kilburn" <dkilburn@rcn.com>

OWL is a perfectly good level at which to define an interpret 
biologically-relevant relationships as human curators.  BioPAX I think 
is a good example of classes and properties that allow us to describe 
quite unambiguously and in human readable phrases, the ordinary meaning 
of what has been captured.

In saying that, I think description logic(what OWL is based on) maybe a 
misnomer in some contexts, I have yet to believe logic can capture or 
describe our ordinary reasoning, but instead is a way of helping us to 
clarify and evaluate it, so that it can evolve.

Processing it from serialized XML form is a darker boundary :-)

cheers
Matt


On 10/08/2004, at 4:17 PM, Dan Kilburn wrote:

> 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.
>
>  
>
> Cheers,
>
> Dan
>
>  
>
>
> From: public-semweb-lifesci-request@w3.org 
> [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of Internet 
> Business Logic
> 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
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Received on Tuesday, 10 August 2004 05:11:54 GMT

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