- From: Jim McCusker <mccusj@rpi.edu>
- Date: Thu, 15 May 2014 18:04:01 -0400
- 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
- Message-ID: <CAAtgn=TwPA0Hat3+zkgeoOZPS=wGPfm3y2ACE4ONt5gvQCk7ag@mail.gmail.com>
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. > > > *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: 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