Re: Clinical terminologies to OWL

Hi

Conversions of  SNOMED CT to OWL may be of interest.
Indeed existing conversions of  SNOMED CT use EL++, which may shortly
become a new 'profile' of  OWL 2 that is, a sublanguage of the
standard.
Though less expressive than OWL DL,  EL++ seems enough for SNOMED CT.
In particular it includes property chain inclusion, useful for
expressing propagation of one property e.g. location along another
e.g. part-of

- Regarding practical results/benefits, see for example slide 19-20 of
http://clarkparsia.com/talks/semweb-tech-in-practice/

- Below quite recent 2007 2008 reference about SNOMED CT in OWL-EL++  and EL++:

[SNOMED EL+]
Replacing SEP-Triplets in SNOMED CT using Tractable Description Logic Operators.
B. Suntisrivaraporn, F. Baader, S. Schulz, K. Spackman, AIME 2007

[EL++]
Pushing the EL Envelope. Franz Baader, Sebastian Brandt, and Carsten
Lutz. In Proc. of the 19th Joint Int. Conf. on Artificial Intelligence
(IJCAI 2005), 2005. [EL++ Update]
Pushing the EL Envelope Further. Franz Baader, Sebastian Brandt, and
Carsten Lutz. In Proc. of the Washington DC workshop on OWL:
Experiences and Directions (OWLED08DC), 2008.

Christine

2008/7/24 John Madden <john.madden@me.com>:
> 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.
>>
>>
>>
>>
>>
>>
>
>
>



-- 
Christine

Received on Friday, 25 July 2008 13:02:02 UTC