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

From: David Booth <david@dbooth.org>
Date: Fri, 16 May 2014 11:42:10 -0400
Message-ID: <537631D2.3060208@dbooth.org>
To: Marc Twagirumukiza <marc.twagirumukiza@agfa.com>, amallia@edmondsci.com
CC: "cnanjo@cognitivemedicine.com" <cnanjo@cognitivemedicine.com>, "eric@w3.org" <eric@w3.org>, "michel.dumontier@gmail.com" <michel.dumontier@gmail.com>, "Peter.Hendler@kp.org" <Peter.Hendler@kp.org>, "public-semweb-lifesci@w3.org" <public-semweb-lifesci@w3.org>, "Rafael.Richards@va.gov" <Rafael.Richards@va.gov>
Hi Marc,

I would encourage you -- and anyone else interested in this topic -- to 
join the Tuesday 11:00am HCLS conference calls if you can.  It's a good 
opportunity to share ideas, and it would be great to have your input. 
We are all figuring this out as we go along, so the more eyes and ideas 
we can put on this the better.  The calls are:

 > Tuesdays, 11:00am Eastern US (Boston) time zone
 > Zakim (W3C teleconference bridge).
 > Dial-In #: _+1.617.761.6200_ <tel:%2B1.617.761.6200> (Cambridge, MA)
 > VoIP address: _sip:zakim@voip.w3.org_ <mailto:sip%3Azakim@voip.w3.org>
 > Participant Access Code: 4257 ("HCLS")
 > IRC: _irc.w3.org_ <http://irc.w3.org/> port 6665 channel #HCLS

Thanks,
David

On 05/16/2014 10:29 AM, Marc Twagirumukiza wrote:
> Dear Anthony
> Thanks a lot for this feedback.
> We have been interested to join this effort of drafting FHIR ontology
> but we missed probably the momentum.
> One of the ideas we had for this effort was to suggest re-use existing
> ontology and not recreate a specific ontology.
> Some good candidate are like the ScheMed
> (https://github.com/twamarc/ScheMed) ontology we were working on in
> collaboration with schema.org (http://schema.org <http://schema.org/> &
> http://blog.schema.org <http://blog.schema.org/>  &
> http://schema.org/MedicalEntity) .
> Hope we will have opportunity and space to discuss this in a specific
> working group.
>
>
> Kind Regards,
> *
> Marc Twagirumukiza, MD, PhD | **Agfa HealthCare*
> Senior Clinical Researcher | HE/Advanced Clinical Applications Research
> T  +32 3444 8188 | M  +32 499 713 300
>
> http://www.agfahealthcare.com <http://www.agfahealthcare.com/>
> http://blog.agfahealthcare.com <http://blog.agfahealthcare.com/>
> ------------------------------------------------------------------------
> Click on link to read important disclaimer:
> http://www.agfahealthcare.com/maildisclaimer
>
>
>
> From:  Anthony Mallia <amallia@edmondsci.com>
> To:  Marc Twagirumukiza/AXPZC/AGFA@AGFA
> Cc:  "cnanjo@cognitivemedicine.com" <cnanjo@cognitivemedicine.com>,
> "david@dbooth.org" <david@dbooth.org>, "eric@w3.org" <eric@w3.org>,
> "michel.dumontier@gmail.com" <michel.dumontier@gmail.com>,
> "Peter.Hendler@kp.org" <Peter.Hendler@kp.org>,
> "public-semweb-lifesci@w3.org" <public-semweb-lifesci@w3.org>,
> "Rafael.Richards@va.gov" <Rafael.Richards@va.gov>
> Date:  16/05/2014 16:09
> Subject:    RE: Propose an HL7 work group on RDF for Semantic
> Interoperability?
> ------------------------------------------------------------------------
>
>
>
> Marc,
> There is not a location so far for posting any material – it is at an
> early stage.
>
> Tony Mallia
>
> *From:* Marc Twagirumukiza [mailto:marc.twagirumukiza@agfa.com] *
> Sent:* Friday, May 16, 2014 4:17 AM*
> To:* Anthony Mallia*
> Cc:* cnanjo@cognitivemedicine.com; david@dbooth.org; eric@w3.org;
> michel.dumontier@gmail.com; Peter.Hendler@kp.org;
> public-semweb-lifesci@w3.org; Rafael.Richards@va.gov*
> Subject:* RE: Propose an HL7 work group on RDF for Semantic
> Interoperability?
>
> Dear Anthony,
> Do you know where we can find documentation/resources about the ongoing
> work  FHIR ontology ?
>
> Kind Regards,*
>
> Marc Twagirumukiza, MD,PhD | **Agfa HealthCare*
> Senior Clinical Researcher | HE/Advanced Clinical Applications Research
> T  +32 3444 8188 | M  +32 499 713 300
> _
> __http://www.agfahealthcare.com_ <http://www.agfahealthcare.com/>_
> __http://blog.agfahealthcare.com_ <http://blog.agfahealthcare.com/>
>
> ------------------------------------------------------------------------
>
> Click on link to read important disclaimer:
> _http://www.agfahealthcare.com/maildisclaimer_
>
>
>
> From:        Anthony Mallia <_amallia@edmondsci.com_
> <mailto:amallia@edmondsci.com>>
> To:        "_Peter.Hendler@kp.org_ <mailto:Peter.Hendler@kp.org>"
> <_Peter.Hendler@kp.org_ <mailto:Peter.Hendler@kp.org>>,
> "_michel.dumontier@gmail.com_ <mailto:michel.dumontier@gmail.com>"
> <_michel.dumontier@gmail.com_ <mailto:michel.dumontier@gmail.com>>
> Cc:        "_david@dbooth.org_ <mailto:david@dbooth.org>"
> <_david@dbooth.org_ <mailto:david@dbooth.org>>, "_eric@w3.org_
> <mailto:eric@w3.org>" <_eric@w3.org_ <mailto:eric@w3.org>>,
> "_cnanjo@cognitivemedicine.com_ <mailto:cnanjo@cognitivemedicine.com>"
> <_cnanjo@cognitivemedicine.com_ <mailto:cnanjo@cognitivemedicine.com>>,
> "_Rafael.Richards@va.gov_ <mailto:Rafael.Richards@va.gov>"
> <_Rafael.Richards@va.gov_ <mailto:Rafael.Richards@va.gov>>,
> "_public-semweb-lifesci@w3.org_ <mailto:public-semweb-lifesci@w3.org>"
> <_public-semweb-lifesci@w3.org_ <mailto:public-semweb-lifesci@w3.org>>
> Date:        15/05/2014 22:50
> 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>
> [_mailto:Peter.Hendler@kp.org_] *
> Sent:* Tuesday, May 13, 2014 5:33 PM*
> To:* _michel.dumontier@gmail.com_ <mailto:michel.dumontier@gmail.com>*
> Cc:* _david@dbooth.org_ <mailto:david@dbooth.org>; Anthony Mallia;
> _eric@w3.org_ <mailto:eric@w3.org>; _cnanjo@cognitivemedicine.com_
> <mailto:cnanjo@cognitivemedicine.com>; _Rafael.Richards@va.gov_
> <mailto:Rafael.Richards@va.gov>; _public-semweb-lifesci@w3.org_
> <mailto: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.
>
>
>
> *
>
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>
> From:        Michel Dumontier <_michel.dumontier@gmail.com_
> <mailto:michel.dumontier@gmail.com>>
> To:        David Booth <_david@dbooth.org_ <mailto:david@dbooth.org>>
> Cc:        Anthony Mallia <_amallia@edmondsci.com_
> <mailto:amallia@edmondsci.com>>, "Prud'hommeaux, Eric" <_eric@w3.org_
> <mailto:eric@w3.org>>, Claude Nanjo <_cnanjo@cognitivemedicine.com_
> <mailto:cnanjo@cognitivemedicine.com>>, "Richards, Rafael M.
> (_Rafael.Richards@va.gov_ <mailto:Rafael.Richards@va.gov>)"
> <_Rafael.Richards@va.gov_ <mailto:Rafael.Richards@va.gov>>, w3c semweb
> HCLS <_public-semweb-lifesci@w3.org_ <mailto: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_
> <mailto: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_ <tel:%2B1.617.761.6200> (Cambridge, MA)
> VoIP address: _sip:zakim@voip.w3.org_ <mailto:sip%3Azakim@voip.w3.org>
> Participant Access Code: 4257 ("HCLS")
> IRC: _irc.w3.org_ <http://irc.w3.org/> port 6665 channel #HCLS
>
> Thanks,
> David
Received on Friday, 16 May 2014 15:42:42 UTC

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