Re: [VM] Natasha and Alan
"Goldeen Bell" <[email protected]> Thu, 04 Nov 2004 01:23:14 -0500
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Thomas<BR><BR>I am something of a stand-in for the experience of the medica= l community. There are several relevant groups to point at alth= ough I am not in a position to write a definitive paper on any of them:<BR>= <BR>SNOMED-CT (and its ancestor in the UK Clinical Terms) - the officially = mandated terminology<BR><BR>HL7 (the main healthcare information standards = body) Vocabulary group which manages a variety of terminologies.<BR><BR>The= National Cancer Institute's Metathesaurus<BR><BR>The Unified Medical Langu= age system<BR><BR>The Gene Ontology and the Open Bio Ontologies (OBO) group= more generally.<BR><BR>In all these cases the interest would be in the pri= nciples, issues and use cases encountered, e.g. tracking versions, handling= of retired terms, handling of splitting and joining terms, when a change o= f a label indicates a new concept, etc. None of them use URIs as iden= tifiers. HL7 uses OIDs, SNOMED has its own system of 64 bit - or perh= aps now more - identifiers partitioned up so as to allow a name-space like = construct. All make a sharp separation between 'concept' and 'term', = and use separate 'nonsemantic' identifiers for each. All use "p= re-web" technology.<BR><BR>The other work in the medical area which may hav= e an impact in this area is Mayo Clinic's work on the terminology services = engine, CTS. The best thing on that is to contact Harold = Solbrig directly whom I am copying on this email.<BR><BR>SNOMED had s= everal papers on their updating procedure that used to be on their web site= during development, but they seem to have disappeared. I can see if = I can retrieve any of them, although they may be considered commercial conf= idential.<BR><BR>The strongest line in the medical community - because grou= p after group has had to rediscover it or at least rediscover that the comm= unity was right - is to separate the "concept" and "term" and to use "meani= ngless" identifiers of some sort which are not subject to problems of argum= ents over spelling, differences in usage between communities, etc. &nb= sp; Also never, ever, to re-use an identifier.<BR><BR>I am not quite sure h= ow this translates into the Semantic Web world. The rdf:label propert= y is a relatively weak mechanism, e.g. as far as I know it is just st= ring valued and there is no inverse, so that the notion of going from label= to concept isn't really supported, nor any notion of labels in their own r= ight. There is also no obvious notion of "preferred term" - something= the medical community has found essential as soon as you start to allow mu= ltiple labels. Potentially the language field could be used for this = purpose, but this really needs testing against the use cases.<BR><BR>The cl= assic paper, although way pre-web is Cimino's Desiderata paper Methods of I= nformation in Medicine37(4-5): pp. 394-403. Some of the issues are clearly = parochial to medicine, but others seem entirely general.<BR><BR>Regards<BR>= <BR>Alan<BR><BR>Thomas Baker wrote:<BR><BR>> Natasha, Alan,<BR>><BR>&= gt; On the basis of previous discussion of the VM draft, it<BR>> was cle= ar to me exactly what role you would want to have in<BR>> the paper.<BR>= ><BR>> Note that in its current form, the draft is set up to cite<BR>= > practices from a handful of example vocabularies (FOAF, Dublin<BR>>= Core, SKOS, etc) to illustrate some general principles.<BR>><BR>> I = was wondering whether, between the two of you, there is<BR>> a major voc= abulary in medicine or the life sciences about<BR>> which you would be w= illing to provide some explanatory text<BR>> and references (with regard= to use of URI references, formal<BR>> schemas, etc). Having one r= eally large-scale, tightly designed<BR>> ontology would be perfect to ro= und out the set of examples.<BR>><BR>> Any other ideas most welcome.<= BR>><BR>> Thank you,<BR>> Tom<BR>><BR>> > &nbs= p; -- A major medical or life-sciences vocabulary?<BR>> >= TASK: Alan or Natasha - An= example of a large-scale ontology?<BR>> > &nb= sp; Do we perhaps need another major ex= ample? It would<BR>> >  = ; be good to have a "large-scale" vocabulary of the= <BR>> > &n= bsp; "ontology" sort, preferably with some well-defined<BR>> > &= nbsp; maintenance and= versioning policies...<BR>><BR>> --<BR>> Dr. Thomas Baker &n= bsp;  = ; <A href=3D"mailto:T= homas.Baker%40izb.fraunhofer.de?Subject=3DRe%3A%20%5BVM%5D%20Natasha%20and%= 20Alan&In-Reply-To=3D<4180DA03.118CD2F3%40cs.man.ac.uk>&References= =3D<4180DA03.118CD2F3%40cs.man.ac.uk>">[email protected]</A><B= R>> Institutszentrum Schloss Birlinghoven &= nbsp; mobile +49-160-9664-2129<BR>> Fraunhofer-Gesellschaft&= nbsp; &nbs= p; = work +49-30-8109-9027<BR>> 53754 Sankt Augustin, Germany &nbs= p; &= nbsp; fax +49-2241-144-2352<BR>> Personal email: <A hr= ef=3D"mailto:thbaker79%40alumni.amherst.edu?Subject=3DRe%3A%20%5BVM%5D%20Na= tasha%20and%20Alan&In-Reply-To=3D<4180DA03.118CD2F3%40cs.man.ac.uk>&= ;References=3D<4180DA03.118CD2F3%40cs.man.ac.uk>">[email protected].= edu</A><BR><BR>--<BR>Alan L Rector<BR>Professor of Medical Informatics<BR>D= epartment of Computer Science<BR>University of Manchester<BR>Manchester M13= 9PL, UK<BR>TEL: +44-161-275-6188/6149/7183<BR>FAX: +44-161-275-6236/6204<B= R>Room: 2.88a, Kilburn Building<BR>email: <A href=3D"http://binary-search.o= rg/">[email protected]</A><BR>web: <A href=3D"http://enter-se.com/">www.c= s.man.ac.uk/mig</A><BR> <A href= =3D"http://seek-time.org/">www.opengalen.org</A><BR>  = ; <A href=3D"http://search-options.com/">www.clinical-esc= ience.org</A><BR> <A href=3D"http= ://your-search.org/">www.co-ode.org</A><BR><BR> --=20 <p>___________________________________________________________<br>Sign-up f= or Ads Free at Mail.com<br> <a href=3D"http://mail01.mail.com/scripts/payment/adtracking.cgi?bannercode= =3Dadsfreejump01" target=3D"_blank">http://www.mail.com/?sr=3Dsignup</a></p>