Re: Clinical terminologies to OWL

Jyoti,

Thanks for the reference. I agree the paper makes some good points.

A promising alternative to deal with legacy graph-based formalisms  
with hierarchies and otherwise sparse axiomatization (of which SNOMED  
is one example) and still provide "upward mobility" to OWL is the  
RDFS(FA) proposal (http://dl-web.man.ac.uk/rdfsfa/). I think this  
website is a "must-read" for those of us interested in this sort of  
thing, and a more powerful alternative target language for such legacy  
vocabs than the other alternative I mentioned of just using skos  
descriptors.

(btw Vipul: RDFS(FA) is also extremely relevant to a parallel thread  
going on here about "multi-layered KR", as it is designed to separate  
instance modeling from class modeling in a way that is much more akin  
to UML than is possible in RDFS).


John


On Jul 24, 2008, at 2:00 PM, Jyotishman Pathak wrote:

> Hello John,
>
> I think these are very interesting ideas.
>
> While we are at the topic of representing SNOMED in OWL-DL (I am  
> assuming you are referring to OWL-DL 1.0), I would like to point to  
> a paper by Kent Spackman published in 2007: http://www.webont.org/owled/2007/PapersPDF/submission_26.pdf
>
> In the paper, Kent gives insights on how OWL-DL 1.0 may not be  
> adequate to model SNOMED. So, while I agree that "It is far less  
> expressive than OWL" (SNOMED falls in EL++ logic), there are certain  
> elements in SNOMED as of now that cannot be expressed by OWL-DL 1.0.
>
> Cheers,
> - Jyoti
>
>
>
> On Thu, Jul 24, 2008 at 12:35 PM, John Madden <john.madden@me.com>  
> wrote:
>
> Hey Chime,
>
> Thanks for coming up with this project task proposal relating to  
> conversion of legacy terminologies to OWL/RDF, it's very exciting.
>
> I really like your idea of picking a specific subdomain, like drug  
> terminology, and using that to test out the pitfalls/possibilities.
>
> (Actually, I think very domain-specific ontolgies have, as a rule,  
> the strongest likelihood of short-term practical utility.)
>
> We (Mary and I) have an ongoing project involving cancer reporting  
> for public health where I've always dreamed of producing an OWL/RDF  
> adaptation of content culled from a variety of sources including  
> SNOMED CT, and also others. Unlike the NIH cancer ontology which  
> includes a lot of biosicence related content, we'd focus exclusively  
> on supporting routine clinical aspects of cancer care.
>
> I'd love to make this a use case. It does involve modeling some  
> "utility" classes and relations (like Patient, Physician, etc.) but  
> I'd like to move that stuff out into some more generic project.
>
> (As Vipul knows, modeling that stuff always involves taking  
> appropriate cognizance of constitutencies at HL7, CDISC, CaBIG, etc.  
> etc. -- although I think it would be grand just to demonstrate to  
> the world that it is possible to do this without stepping on  
> anyone's toes through the judicious use of imports, sameAs/  
> differentFrom, equivalentClass, seeAlso, etc).
>
> John
>
> P.S. w.r.t SNOMED CT, to just clarify the point I in the call today  
> about whether there would ever be an OWL-SNOMED: the expressivity of  
> the DL underlying SNOMED is roughly on a par with that of RDFS. It  
> is far less expressive than OWL. I could therefore imagine an RDF- 
> SNOMED, but not an OWL-SNOMED.
>
> Anyway, unlike RDF/S, SNOMED has never had a published formal  
> semantics, and certainly not a model-theoretic one like RDF/OWL's.  
> (Indeed, the absence of an explicit model-theoretic semantics makes  
> the claim that SNOMED is DL-based at all pretty fuzzy-wuzzy. I'd  
> maintain this is so even though, in practice, each SNOMED CT release  
> has to classify on the ontylog reasoner.) Hence my remark earlier  
> that it might be safest just to consider SNOMED concepts, if  
> represented as resources, as being instances of skos:Concept.
>
>
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