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

From: <Peter.Hendler@kp.org>
Date: Thu, 15 May 2014 16:48:03 -0700
To: mccusj@rpi.edu
Cc: amallia@edmondsci.com, cnanjo@cognitivemedicine.com, david@dbooth.org, eric@w3.org, michel.dumontier@gmail.com, public-semweb-lifesci@w3.org, Rafael.Richards@va.gov
Message-ID: <OF06D8856A.A0348856-ON88257CD9.00828CC4-88257CD9.0082BE51@kp.org>
Yes there is a formal mapping. If you download SNOMED from the NLM there 
will be a PERL script written by Kent Spackman somewhere in there. It will 
use the official release files and generate an OWL file. That is the 
official mapping.  The Plus in EL+ I used to know. I think it means 
hierarchical roles and role groups.  Or maybe it was role chaining. It was 
one of those things with roles.


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From:   Jim McCusker <mccusj@rpi.edu>
To:     Peter Hendler/CA/KAIPERM@KAIPERM
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
Date:   05/15/2014 03:04 PM
Subject:        Re: Propose an HL7 work group on RDF for Semantic 
Interoperability?



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] 
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. 





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From:        Michel Dumontier <michel.dumontier@gmail.com> 
To:        David Booth <david@dbooth.org> 
Cc:        Anthony Mallia <amallia@edmondsci.com>, "Prud'hommeaux, Eric" <
eric@w3.org>, Claude Nanjo <cnanjo@cognitivemedicine.com>, "Richards, 
Rafael M. (Rafael.Richards@va.gov)" <Rafael.Richards@va.gov>, w3c semweb 
HCLS <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 


On Tue, May 13, 2014 at 7:54 AM, David Booth <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 (Cambridge, MA)
VoIP address: sip:zakim@voip.w3.org
Participant Access Code: 4257 ("HCLS")
IRC: 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 23:49:08 UTC

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