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RE: [HCLS] Bridging Ontologies - with Foundational Ontologies

From: Kashyap, Vipul <VKASHYAP1@PARTNERS.ORG>
Date: Tue, 22 Aug 2006 07:47:04 -0400
Message-ID: <2BF18EC866AF0448816CDB62ADF6538104C15EB2@PHSXMB11.partners.org>
To: "Chimezie Ogbuji" <ogbujic@bio.ri.ccf.org>, "Donald Doherty" <donald.doherty@brainstage.com>
Cc: <public-semweb-lifesci@w3.org>


Chimezie,

Is it possible for you to write up this use case and put it on the Ontology Task
Force Wiki?

There could be multiple approaches for bridging ontologies, some pragmatic and
some formal using resources such as the UMLS or DOLCE.

Thanks!

---Vipul

> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org [mailto:public-semweb-lifesci-
> request@w3.org] On Behalf Of Chimezie Ogbuji
> Sent: Monday, August 21, 2006 10:08 PM
> To: Donald Doherty
> Cc: public-semweb-lifesci@w3.org
> Subject: Re: [HCLS] Bridging Ontologies - with Foundational Ontologies
> 
> 
> 
> 
> 
> On Mon, 21 Aug 2006, Donald Doherty wrote:
> 
> > Creating explicit connections between all similar and/or identical
> entries
> > in two schemas is an arduous task that is impractical to do manually.
> 
> Actually, I recently had quite a good experience doing this same thing
> with trying to align top-level concepts of a Patient Record ontology with
> a 'foundational ontology'.  There was a recent email [1] on this mailing
> list about bio-zen that [2] caught my attention because it specifically
> uses DOLCE [3] as a foundational ontology. I like the approach because it
> causes you to 'ground' your semantics by thinking about them in the most
> fundamental ways..
> 
> In my case, I was connecting my ontology with DOLCE
> in order to formalize the domain independent terms, but in doing so any
> other ontology grounded
> in this way also would be largely interoperable.
> 
> For example, for the concept of a diagnosis, I found DOLCE's
> dol:information-realization class appropriate.
> 
> " Any physical entity that realizes an information object. "
> 
> So, the act that records the diagnosis is an dol:information-realization
> which 'realizes' (dol:realize) a specific kind of information-object.  The
> information-object class tree is:
> 
> * information-object
>    * diagrammatic-object
>    * iconic-object
>    * linguistic-object
>      * word
>      * phoneme
> 
> dol:linguistic-object seemed most appropriate given it's definition:
> 
> " An information object ordered by (encoded according to) a language.  "
> 
> Where the ordering is with respect to Pathology.  So the act that
> realizes a diagnosis (an angiogram, clinical exam, lab test, etc..) and
> the diagnosis itself can be aligned with a foundational ontology in this
> way.
> 
> Ofcourse, a foundational ontology is only as useful as it is well
> organized and I've found DOLCE to be pretty methodical in it's
> arrangement (but I found myself refering to CyC and SUMO occasionally
> where DOLCE didn't have any decent definition for a concept)
> 
> Since it models at a very linguistic and congitive level, the nomenclature
> might seem a bit odd at first (perdants, endurants, spacio-temporal
> things, and what not) but I was able to find an appropriate place for most
> of the top-level concepts I attempted to align.
> 
> Unfortunately, bio-zen was more oriented to concepts at the molecular
> level than for my needs, but any connection made to DOLCE would
> automatically orient themselves with bio-zen (or any other derivatives).
> 
> > To contrast, compare, and reconcile at the data level I must make these
> > explicit connections.
> >
> > When I do so mentally, I make a tentative connection, test it for
> validity,
> > and then maintain the connection or throw it out based on the result.
> (This
> > is also what is done physiologically through mechanisms like Long Term
> > Potentiation in the brain.)
> >
> > Automate connections between synonyms, antonyms, etcetera based on local
> > analysis of elements.
> 
> As a matter of fact, DOLCE has a rather impressive mapping [4] to wordnet
> 1.6 that could (in theory - having only browsed this mapping) facilitates
> some of this by virtue of wordnet's impressive lexical coverage.
> 
> [1] http://lists.w3.org/Archives/Public/public-semweb-
> lifesci/2006Jul/0088.html
> [2] http://neuroscientific.net/index.php?id=download
> [3] http://www.loa-cnr.it/DOLCE.html (DOLCE)
> [4] http://www.loa-cnr.it/Files/OWN_description.txt (OntoWordNet)
> 
> Chimezie Ogbuji
> Lead Systems Analyst
> Thoracic and Cardiovascular Surgery
> Cleveland Clinic Foundation
> 9500 Euclid Avenue/ W26
> Cleveland, Ohio 44195
> Office: (216)444-8593
> ogbujic@ccf.org
> 
Received on Tuesday, 22 August 2006 11:47:29 GMT

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