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

I am an ardent and reverent disciple of the position Jim outlines  
below.	:-)

This is the point I was trying to make in my response to an issue  
brought up a few days back re: the relation between the BioRDF data  
sets being identified/converted and their relation to the BioONT's  
efforts identifying what I was referring to as distilled knowledge  
resources (DKR) - a neologism designed to shed some of the baggage  
artifacts such as terminologies, taxonomies, classification schemes,  
thesauri, and ontologies bring with them - though I'm probably just  
making matters worse by adding another term to the bag.

I like to think we are converging on systems of ever increasing,  
emergent "intelligence" as we work to combine these approaches -  
which would include in the cornucopia of research domains:
	- statistically-based data mining techniques (customized for  
different types of data such as sequence analysis, gene expression  
analysis, computer vision algorithms applied to automatically  
extracting biologically relevant shapes from bioimaging data sets,  
Bayesian analysis applied to time-series physiological data, etc.)
	- modeling techniques - pathway modeling, physiological modeling  
from molecules on up through systems, morpho-anatomical modeling, etc.
	- Text-based KE/KR/KM - e.g., NLP, LSI, enhanced IR of all sorts, etc.
	- the related field of computational linguistics and lexical  
analysis informing the creation of CVs, taxonomies, classification  
schemes, and thesauri
	- logic formalisms - DL, Rule-based, etc. - used both for bottom-up  
& top-down KE/KR/KM

I've been taking this line, since the time when I was head of product  
development for the Biological Abstracts (BIOSIS) in the mid-90s and  
further in ontological engineering work I did in the late 90s with  
the bioinformatics company DoubleTwist.

This is the editorializing I was avoiding in my initial forwarded  
post.  ;-)

Cheers,
Bill



On Jan 20, 2007, at 8:11 PM, Jim Hendler wrote:

> While I think there's a lot of iteresting issues in this space, let  
> me point out that the mail below seems to think that the "OR"  
> between top-down and bottom-up is an "XOR" - i.e. one of the  
> other.  The vision I've been pushing for a long time is one where  
> they both flourish, and even more importantly they link together  
> into a Web of Semantic Definitions.   My very first briefs when the  
> DAML language was being created included the idea that a key aspect  
> of a "distributed ontological representation" was that it could  
> combine top-down and bottom-up approaches - here's the words from a  
> slide from 2000 - you can see I've been saying this for a long time  
> now...
>  -Jim H.
> p.s. For US readers, this is one of the arguments that helped  
> convince the govt to spend a chunk of your tax dollars on creating  
> an ontology language :-)
>
> (from DARPA presentation - ca. 2000 - apologies for formatting,  
> copiy/pasted from a slide in ppt format)
>
> Small communities define common semantics
> Technical Vocabularies abound
> Mission specific
> Technical jargons
> Shared values
> Larger communities form around shared terms
> Mapping and "articulation" become crucial
> Interoperability at web languages level
> Top-Down (organization defines critical aircraft properties)
>          or bottom up (Oh, a "foxbat" is a Mig29)
> Business case for improving communication!
>
>
> At 11:14 AM -0500 1/20/07, Kashyap, Vipul wrote:
> 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>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>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>http://www.openclinical.org/medTermUmls.html).
>
> Cheers,
> Bill
>
> Begin forwarded message:
>
>
> From: <mailto:gary.h.merrill@GSK.COM>gary.h.merrill@GSK.COM
> Date: January 19, 2007 10:52:11 AM EST
> To: <mailto:UMLSUSERS-L@LIST.NIH.GOV>UMLSUSERS-L@LIST.NIH.GOV
> Subject: Re: MRHIER and AUIs
> Reply-To: <mailto:gary.h.merrill@GSK.COM>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 -  
> <mailto:William.Bug@DrexelMed.edu>William.Bug@DrexelMed.edu
>
>
>
>
>
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> -- 
> Prof James Hendler				hendler@cs.rpi.edu
> Tetherless World Constellation Chair		http://www.cs.umd.edu/~hendler
> Computer Science Dept			301-405-2696 (work)
> Rensselaer Polytechnic Inst			301-405-6707 (Fax)
> Troy, NY 12180

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