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RE: [OPEN] and/or [PORT] : a practical question

From: Bernard Vatant <bernard.vatant@mondeca.com>
Date: Thu, 25 Mar 2004 11:02:04 +0100
To: "SWBPD" <public-swbp-wg@w3.org>
Message-ID: <GOEIKOOAMJONEFCANOKCGECMDKAA.bernard.vatant@mondeca.com>


> I am not sure if Bernard's concern is only about subject hierarchies
> or about mixing ontologies and terminologies in general.

My question was explicitely about the former in this thread, but my general concern is
about the latter, definitely.

> If it is the former, than the message below is not very relevant.

I found it pretty much relevant :))

> For the latter,
> here are a few words from the experience in a number of
> medical-informatics projects in our lab. In our experience, the issue
> of linking ontologies and terminologies comes up often. There is no
> lack of (often reasonably well-structured) controlled terminologies
> in medical informatics, using them makes sense both from reusability
> and interoperability perspectives. However, in our projects and their
> ontologies, it inevitably led to mixing classes and instances, and we
> really didn't find any practical workarounds (although admittedly we
> were not wedded to DLs, so didn't look too hard).
> Consider for example clinical guidelines (again, this is a practical
> example from a couple of kb-based systems here). A specific clinical
> guideline (an instance of a class Clinical Guideline) represents the
> tests, decisions, etc. in diagnosing and treating a particular
> ailment. One of the reference terminologies used here is that of
> drugs. (cf Chris's message later: a drug hierarchy is not a
> partonomy, it is indeed a subclass hieararchy. You have
> beta-clockers, and specific types of beta-blockers as subclasses,
> etc.). So, a specific instance of a clinical guideline must refer to
> classes of drugs to be prescribed. Again, at a particular step in a
> guideline you want to prescribe a specific beta-blocker. But you want
> this guideline to be retrieved when looking for all guidelines using
> beta-blockers. Note, the guideline really refers to a class of drugs
> and not a specific bottle with pills.

I understand quite well your example, having working myself two years ago in this field,
on a drug development model for a major company, including various aspects such as
physico-chemical properties, bio-chemical targets, clinical activity, assays of all kinds,
patents, production process, formulation ... and we've been through tricky issues
generated by so many different views of the 'same' drug in so many different contexts :
generic molecule, or family of molecules with hundreds of variant forms, or specific
batches from a specific production process, or specific formulation or commercial name ...
>From so many various viewpoints, it's obvious that a simple and fit-all representation is
very difficult to apply, 'sameness' has to be addressed at a very pragmatic level. And of
course, it includes re-use of legacy (like MeSH and the like). And sticking to DL in such
a context is barely possible.

Actually, the specific issue of class as document subject is dreadfully simple in
comparison ...

> Hope this helps.

I think it is.

Bernard Vatant
Senior Consultant
Knowledge Engineering
Mondeca - www.mondeca.com
Received on Thursday, 25 March 2004 05:02:12 EST

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