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RE: [HCLS] Bridging Ontology...An Automated Approach?

From: Mork, Peter D.S. <pmork@mitre.org>
Date: Tue, 22 Aug 2006 09:04:23 -0400
Message-ID: <224FBC6B814DBD4E9B9E293BE33A10DC011776EF@IMCSRV5.MITRE.ORG>
To: "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>, "William Bug" <William.Bug@DrexelMed.edu>
Cc: <donald.doherty@brainstage.com>, <public-semweb-lifesci@w3.org>
I second the request for specific examples because, in my experience,
most mediators rely on a logical data model with queries (SQL or
XQuery) mapping the underlying data models into the mediated model.  In
some cases (e.g., TAMBIS), the mediating model is actually an ontology,
but this is rare.  The mappings themselves are expressed in a language
with sophisticated transformative capabilities because of the myriad
incompatibilities that exist.  For example, aggregation is not
supported by many rule or ontology languages.  Neither are regular
expressions.

 

Peter Mork

 

________________________________

From: Kashyap, Vipul [mailto:VKASHYAP1@PARTNERS.ORG] 
Sent: Tuesday, August 22, 2006 8:57 AM
To: William Bug; Mork, Peter D.S.
Cc: donald.doherty@brainstage.com; public-semweb-lifesci@w3.org
Subject: RE: [HCLS] Bridging Ontology...An Automated Approach?

 

We are using mediation technology within the BIRN project as well.  It
has many ways in which it can solve some of the problems we're
discussing.

 

My fear is every new repository requires an new mapping/registration to
the mediator and/or shared ontology.  This can be a very fragile system
over time, and - as you point out, Peter, tacit assumptions in the
source data models (and their use of semantics) - which of course can
also change - may greatly limit the depth and breadth with which
queries can be mapped to all the data sources.

 

Semantic web approaches appear to circumvent some of the technical
frailties, though I don't think they can necessarily overcome the
requirement for shared foundational and generic ontology layers.

 

[VK] It will be great if you could give some use cases on how Semantic
web approaches can help circumvent the fragility of the system,
requiring mappings and registrations...

 

 

On Aug 22, 2006, at 7:52 AM, Mork, Peter D.S. wrote:

 

 

		Creating explicit connections between all similar
and/or identical

	entries

		in two schemas is an arduous task that is impractical
to do

manually.

	 

	[VK] Will mapping each of these schemas to an ontology and then
using

the

	ontology to mediate further queries help alleviate the problem?

	 

	---Vipul

	 

	 

 

This is the approach adopted by caBIG.  Individual data models (or

schemata) are related to a common ontology.  By itself, this doesn't

allow one to rewrite queries (because of tacit assumptions present in

the respective data models?), but the hope is that development of

query-mediators will be facilitated by the existence of a loose

mapping.

 

Peter

 

 

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

 

 

 

 



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Received on Tuesday, 22 August 2006 13:08:58 GMT

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