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Comments on the tension between bottom-up KR and use of top down ontologies

From: William Bug <William.Bug@DrexelMed.edu>
Date: Sat, 20 Jan 2007 10:01:56 -0500
To: public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>
Message-Id: <2EE9B3DD-34C8-479A-8BCB-27C843371506@DrexelMed.edu>
Hi All,

This was recently posted to the UMLS list.

Given some of the issues we've been discussing, I thought others  
might appreciate some of the ideas recounted here by Gary Merrill  
from GlaxoSmithKline

I have my own take on this very very important issue, but I'd rather  
not editorialize on Gary's points - and give you a chance to process  
them as he so clearly expressed them.  Some familiarity with UMLS  
structure is helpful (http://umlsinfo.nlm.nih.gov).

By the way, a site relevant to our efforts is the Open Clinical site  
(KM for Medical Care - http://www.openclinical.org/medTermUmls.html).


Begin forwarded message:

> From: gary.h.merrill@GSK.COM
> Date: January 19, 2007 10:52:11 AM EST
> Subject: Re: MRHIER and AUIs
> Reply-To: gary.h.merrill@GSK.COM
> William:
> I think that was a very good non-techincal summary of some issues  
> in the
> Metathesaurus that can be difficult and confusing.  The nature and  
> role of
> AUIs (and their relationships to one another and to the CUIs that they
> "realize") can require substantial thought.
> I am always a little concerned when I see statements such as  "In  
> an ideal
> harmonious world,  NLM and all sources would agree, and Meta would  
> become
> a single unified principled
> ontology."   I do not in fact think that this is necessarily true  
> (under
> some reasonable constraints it is in fact provably false), and  
> definitely
> do not think it should be taken as a disideratum.  Perhaps you do not
> either, but I wanted to take this opportunity to say that,  
> particularly in
> the context of evolving empirical scientific theories, we should not
> expect (and not necessarily even strive for) such a unified ontology.
> (There are, of course, those who would disagree.)  The history of  
> science
> and the history of philosphy has shown the folly of this, and I would
> argue that while striving for a certain "convergence" is desireable,
> striving for the one true theory/ontology is not.  That's something  
> of a
> digression, but I take the strength of UMLS to lie in providing a  
> way of
> "communicating between" and using mulitple disparate (at times  
> mutually
> inconsistent) world views without imposing a strict ueber-ontology.  
> Again,
> there are those who tend to find the lack of the ueber-ontology to  
> leave
> them feeling insecure and adrift in metaphysical ream of uncertainty.
> As I expressed to Chris in separate communication, from my  
> perspective (as
> a very application-oriented user), UMLS provides a usually adequate
> representation of "concepts" (via CUIs), and terms/words/linguistic  
> items
> (via SUIs, LUIs, etc.).  What it does not provide a particularly crisp
> representation of at the moment is "things" -- e.g., diseases  
> rather than
> disease names or disease concepts (that is, the extensional  
> correlate of
> the (intensional) concept/CUI).  AUIs are enlisted to support this  
> to some
> degree, but they are somewhat too closely allied to linguistic items
> (terms) to carry the genuine semantic weight of  
> "things" (extensions).  At
> best, one ends up using sets of AUIs as equivalence classes to  
> represent
> the thing to which each of the AUIs "refers" (though "refer" here  
> is, I
> think, a bit misleading).  So in terms of a classic thing/word/concept
> semantic hierarchy, my feeling is that UMLS does a good job of the
> word/concept part, but the thing part is left a bit "mushy".  However,
> there is room for substantial debate here, and many of the issues are
> unclear.
> Largely this is a consequence of construing UMLS as a -- surprise --
> meta*thesaurus* rather than a meta*ontology*, and focusing on meaning
> relations (e.g., synonomy) rather than more fundamental semantic  
> relations
> (e.g., denotation and extension).   I do have some ideas of how  
> this might
> be addressed, but won't even mention them here -- partly because  
> working
> them out requires substantial thought and care, and partly because  
> I'm not
> altogether sure of what the benefit would be (to most UMLS users) to
> retrofitting such an approach to UMLS.
> ------------------------------
> Gary H. Merrill, Director
> Semantic Technologies Group
> Statistical and Quantitative Sciences
> GlaxoSmithKline Research and Development
> Research Triangle Park, NC
> 919.483.8456

Bill Bug
Senior Research Analyst/Ontological Engineer

Laboratory for Bioimaging  & Anatomical Informatics
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

Received on Saturday, 20 January 2007 15:02:12 UTC

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