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Re: Propose an HL7 work group on RDF for Semantic Interoperability?

From: Jim McCusker <mccusj@rpi.edu>
Date: Thu, 15 May 2014 18:04:01 -0400
Message-ID: <CAAtgn=TwPA0Hat3+zkgeoOZPS=wGPfm3y2ACE4ONt5gvQCk7ag@mail.gmail.com>
To: "peter.hendler" <Peter.Hendler@kp.org>
Cc: amallia@edmondsci.com, cnanjo@cognitivemedicine.com, David Booth <david@dbooth.org>, "Eric Prud'hommeaux" <eric@w3.org>, Michel Dumontier <michel.dumontier@gmail.com>, w3c semweb HCLS <public-semweb-lifesci@w3.org>, Rafael.Richards@va.gov
Is there a formal mapping (and maybe impelementation?) between SNOMED and
OWL EL+? What's been added to the +?

Thanks,
Jim


On Thu, May 15, 2014 at 5:34 PM, <Peter.Hendler@kp.org> wrote:

> On the last point. There is a post coordination syntax for SNOMED (which
> if you understand OWL is really very similar with different syntax).  I'd
> think for the last use case you might as well use the SNOMED post
> coordination syntax. It's actually easier than most representations of OWL,
> and anyone who knows enough SNOMED to post coordinate will certainly know
> this syntax.
>
> For point one, I guess if you wanted to parse your FIHR into a triple
> store that might be nice, but FIHR itself isn't made with ontology in mind.
>  Entities in Roles that Participate in Acts work wonderfully in OWL, But
> Person FIHR resources aren't about those kind of relationships.
>
> Point two. SNOMED is EL+ which is a subset of OWL DL so this can be done,
> but again, the added relationships in FIHR aren't very helpful, and
> besides, EL+ does not scale to millions of patients worth of data for a
> reasoner (it does for SPARQL).  I suppose there is a use case for that..
>  But then it doesn't have to be OWL, it can just be RDF triples.
>
>
> OWL-2RL is massively scalable, but is a different flavor or logic than
> SNOMED.  I like the idea of keeping SNOMED in EL+ and if you do add
> clinical information, then make it Entities in Roles Participating in Acts
> and make it only in OWL-2RL.
>
>
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>
> From:        Anthony Mallia <amallia@edmondsci.com>
> To:        Peter Hendler/CA/KAIPERM@KAIPERM, "michel.dumontier@gmail.com"
> <michel.dumontier@gmail.com>
> Cc:        "david@dbooth.org" <david@dbooth.org>, "eric@w3.org" <
> eric@w3.org>, "cnanjo@cognitivemedicine.com" <cnanjo@cognitivemedicine.com>,
> "Rafael.Richards@va.gov" <Rafael.Richards@va.gov>, "
> public-semweb-lifesci@w3.org" <public-semweb-lifesci@w3.org>
> Date:        05/15/2014 01:53 PM
> Subject:        RE: Propose an HL7 work group on RDF for Semantic
> Interoperability?
> ------------------------------
>
>
>
> Peter,
> Good to see you at the HL7 meeting.
> There seem to be three approaches being worked in RDF
>
> 1.       The first is expressing the FHIR payload in RDF. The ontology is
> therefore the FHIR ontology.. The discussion at HL7 was about making
> another representation of the payload in RDF.
>
> 2.       The second (which I have been working on) has a small sample in
> Protégé is to look at the ontologies of FHIR and Terminologies –
> particularly SNOMED CT and express them together in the same language – OWL
> so that the conflicts can be resolved. The binding from objects in FHIR to
> terms is fundamentally different from the FHIR payload and therefore more
> disruptive. In this approach, a higher ontology is critical – the RIM was a
> start but has quite a lot missing to form a good higher ontology and has
> nothing to do with healthcare (The RIM did not either). It looks as if you
> are going in this direction as well.
>
> 3.       The third which comes from the terminology side is to express
> post-coordinated terms as a code OWL expression in a FHIR message. This is
> a small scope but seems to have some importance to resolving the
> terminology issues.
>
> These three approaches do not overlap or conflict as far as I can see.
>
> Maybe there are two projects one which is aligned to represent FHIR and
> one which looks at the broader issue of Healthcare Ontology as you have
> described. I don’t think the third deserves a project.
>
> Tony Mallia
>
> *From:* Peter.Hendler@kp.org [mailto:Peter.Hendler@kp.org<Peter.Hendler@kp.org>]
>
> * Sent:* Tuesday, May 13, 2014 5:33 PM
> * To:* michel.dumontier@gmail.com
> * Cc:* david@dbooth.org; Anthony Mallia; eric@w3.org;
> cnanjo@cognitivemedicine.com; Rafael.Richards@va.gov;
> public-semweb-lifesci@w3.org
> * Subject:* Re: Propose an HL7 work group on RDF for Semantic
> Interoperability?
>
> We are in fact doing just that at Kaiser on a small experimental scale. We
> are working with Oxford and RDFox and creating an HL7 "RIM Like model".  It
> is not the full RIM but is Entities in Roles Participating in Acts.
>
> I think it would be a mistake to try to put the whole RIM into RDF.  Also
> I'm not a fan of a de novo RDF model that is not based on Entities in Roles
> Participating in Acts, It would then just be an arbitrary other model.  You
> could put FIHR to RDF but I see little reason for it.  Since RDF is wide
> open (almost like saying lets do something in XML) you really have to think
> about what the model is based on before you start.  You've only got V2 (no
> good for RDF) RIM (much too big for RDF) and FIHR (not much advantage to
> RDF for this).
>
> With our "RIM like" model based on Entities in Roles that Participate in
> Acts, we expect to be able to run useful safety and outcome reports.  Also
> we use SNOMED so the ontology of SNOMED will be tightly coupled to our
> model, but our model will not be an extension of the SNOMED model.
>
> I'd be disappointed to see HL7 create a brand new model in RDF that is not
> based on Entities in Roles Participating in Acts.
>
>
>
>
>
> * NOTICE TO RECIPIENT:*  If you are not the intended recipient of this
> e-mail, you are prohibited from sharing, copying, or otherwise using or
> disclosing its contents.  If you have received this e-mail in error, please
> notify the sender immediately by reply e-mail and permanently delete this
> e-mail and any attachments without reading, forwarding or saving them.
>  Thank you.
>
>
>
>
> From:        Michel Dumontier <*michel.dumontier@gmail.com*<michel.dumontier@gmail.com>
> >
> To:        David Booth <*david@dbooth.org* <david@dbooth.org>>
> Cc:        Anthony Mallia <*amallia@edmondsci.com* <amallia@edmondsci.com>>,
> "Prud'hommeaux, Eric" <*eric@w3.org* <eric@w3.org>>, Claude Nanjo <
> *cnanjo@cognitivemedicine.com* <cnanjo@cognitivemedicine.com>>,
> "Richards, Rafael M. (*Rafael.Richards@va.gov* <Rafael.Richards@va.gov>)"
> <*Rafael.Richards@va.gov* <Rafael.Richards@va.gov>>, w3c semweb HCLS <
> *public-semweb-lifesci@w3.org* <public-semweb-lifesci@w3.org>>
> Date:        05/13/2014 02:01 PM
> Subject:        Re: Propose an HL7 work group on RDF for Semantic
> Interoperability?
>
> ------------------------------
>
>
>
>
> David,
>  I'm excited about the prospect, but I think the work group may be a bit
> too broad without further refinement. I'd like to see a charter articulated
> with a more specific focus, and identifying milestones that deliver
> concrete outcomes (specifications, implementations, reports) around
> targeted areas of urgent need.
> More importantly, I'd like to know what the uptake will be (e.g. who will
> implement this), and how plans on using it.
>
> Cheers,
>
> m.
>
>
> Michel Dumontier
> Associate Professor of Medicine (Biomedical Informatics), Stanford
> University
> Chair, W3C Semantic Web for Health Care and the Life Sciences Interest
> Group
> *http://dumontierlab.com* <http://dumontierlab.com/>
>
>
> On Tue, May 13, 2014 at 7:54 AM, David Booth <*david@dbooth.org*<david@dbooth.org>>
> wrote:
> I was at the HL7 meetings last week, and the idea arose of proposing an
> HL7 work group on RDF for Semantic Interoperability.  I took the initiative
> to draft a possible charter.  I meant to send it out earlier in case folks
> would like to discuss the idea on our 11:00am Eastern HCLS call today.
>  Attached is what I've drafted.  I'll join the call and see if anyone wants
> to discuss it.  Sorry for the late notice.
>
> Zakim (W3C teleconference bridge).
> Dial-In #: *+1.617.761.6200* <%2B1.617.761.6200> (Cambridge, MA)
> VoIP address: *sip:zakim@voip.w3.org* <sip%3Azakim@voip.w3.org>
> Participant Access Code: 4257 ("HCLS")
> IRC: *irc.w3.org* <http://irc.w3.org/> port 6665 channel #HCLS
>
> Thanks,
> David
>
>


-- 
Jim McCusker

Data Scientist
5AM Solutions
jmccusker@5amsolutions.com
http://5amsolutions.com

PhD Student
Tetherless World Constellation
Rensselaer Polytechnic Institute
mccusj@cs.rpi.edu
http://tw.rpi.edu
Received on Thursday, 15 May 2014 22:04:47 UTC

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