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

From: Kashyap, Vipul <VKASHYAP1@PARTNERS.ORG>
Date: Sat, 20 Jan 2007 11:14:54 -0500
Message-ID: <2BF18EC866AF0448816CDB62ADF6538105EAF283@PHSXMB11.partners.org>
To: "William Bug" <William.Bug@DrexelMed.edu>, "public-semweb-lifesci hcls" <public-semweb-lifesci@w3.org>
Bill,

 

I am glad you brought this up! This could make a good topic for a future
BIONT/HCLSIG Telcon Agenda.

 

I do have another version of the Top-Down/Bottom-Up "tension" which brings up
the same issue in a different context.

 

Top-Down: Use Cases => Ontologies => Mappings to Data => RDFize Data Sets

Bottom-Up: RDFize Data Sets => Ground RDF Graphs in Ontologies/Terminologies =>
See applicability to Use Cases.

 

Wherea, I do have a preference for one of the above, I do recognize the validity
and appropriateness of the second

approach in various scenarios.

 

Am glad that we are having this debate as a community and if we leverage the
discussions and thoughts proposed

around this, I think we would have made a contribution to the field.

 

Look forward to hearing from fellow HCLSIG-ers on this.

 

Cheers,

 

---Vipul

 

=======================================

Vipul Kashyap, Ph.D.

Senior Medical Informatician

Clinical Informatics R&D, Partners HealthCare System

Phone: (781)416-9254

Cell: (617)943-7120

http://www.partners.org/cird/AboutUs.asp?cBox=Staff&stAb=vik

 

To keep up you need the right answers; to get ahead you need the right questions

---John Browning and Spencer Reiss, Wired 6.04.95

________________________________

From: public-semweb-lifesci-request@w3.org
[mailto:public-semweb-lifesci-request@w3.org] On Behalf Of William Bug
Sent: Saturday, January 20, 2007 10:02 AM
To: public-semweb-lifesci hcls
Subject: Comments on the tension between bottom-up KR and use of top down
ontologies

 

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).

 

Cheers,

Bill

 

Begin forwarded message:





From: gary.h.merrill@GSK.COM

Date: January 19, 2007 10:52:11 AM EST

To: UMLSUSERS-L@LIST.NIH.GOV

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

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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