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RE: Minutes of last week's (Dec 2) HL7 ITS RDF Subgroup / W3C HCLS COI call -- Review of FHIR ontology approaches (cont.)

From: Anthony Mallia <amallia@edmondsci.com>
Date: Sun, 21 Dec 2014 16:30:16 +0000
To: "Peter.Hendler@kp.org" <Peter.Hendler@kp.org>, "kashyap.vipul@gmail.com" <kashyap.vipul@gmail.com>
CC: "david@dbooth.org" <david@dbooth.org>, "grahame@healthintersections.com.au" <grahame@healthintersections.com.au>, "its@lists.hl7.org" <its@lists.hl7.org>, "lloyd@lmckenzie.com" <lloyd@lmckenzie.com>, "public-semweb-lifesci@w3.org" <public-semweb-lifesci@w3.org>
Message-ID: <D5F9B7889182464788941B4EEDE3E81FFD4210A6@Awacs.esci.com>
Peter,
The experiments with the separation of the Ontologies SNOMED, FHIR (Profile) and FHIR instance support the argument not to combine since you can make references across Ontologies without putting them into one.

The OWL Import statement works very well so when you are selecting a SNOMED concept to apply to a FHIR element instance you can see the SNOMED terms but only the binding gets put in the FHIR instance ontology. When you receive the FHIR instance file you can again import the SNOMED Ontology and it will resolve closure on the IRI.

Here is the XML fragment:
<symptom>
……
    <severity value="moderate"/>
</symptom>

Here is a Turtle fragment of a FHIR ReactionSeverity (code) which would be attached to an AdverseReaction.Symptom with a “severity” Object Property
<http://record#01336> rdf:type fhir:ReactionSeverity ,
                      <http://snomed.info/id/6736007> ,
                      owl:NamedIndividual .

The instance of fhir:ReactionSeverity also has a type of SNOMED 6736007
In the SNOMED Ontology, 6736007 is defined:

<http://snomed.info/id/6736007> rdf:type owl:Class ;
                                rdfs:label "Moderate" ;
                                rdfs:subClassOf <http://snomed.info/id/272141005> .

There are various permutations of this – you could also apply rdfs:label “Moderate”  to the ReactionSeverity instance itself.

Tony Mallia


From: Peter.Hendler@kp.org [mailto:Peter.Hendler@kp.org]
Sent: Saturday, December 20, 2014 8:25 PM
To: kashyap.vipul@gmail.com
Cc: david@dbooth.org; grahame@healthintersections.com.au; its@lists.hl7.org; lloyd@lmckenzie.com; public-semweb-lifesci@w3.org
Subject: RE: Minutes of last week's (Dec 2) HL7 ITS RDF Subgroup / W3C HCLS COI call -- Review of FHIR ontology approaches (cont.)

I can think of two reasons why (except maybe in an academic paper or PHD thesis) we would not put SNOMED and the information model in one RDF/OWL Ontology.

One is the idea of keeping the information model, specifically FIHR, very small. The goal is to keep it under 200 resources, closer to 100 even better.
SNOMED has over half a million classes.  I have argued with others who want to put it all in one Ontology that you are adding an ocean to a puddle. You don't need or want all those millions of extra triples riding around in your FHIR.

The other idea has to do with the way people think.  Less than one person in 2000 who does clinical models thinks "open world" and OWL.  Domains and Ranges would be thought of as constraints. Differently named resources would be assumed to be different. There would be many unpredictable modeling and logic errors if people who clearly think in "closed world" database and UML were to start mixing OWL DL logic in the same model. Since the whole mixed ontology would be OWL and not UML or FHIR, there would be many false and unintended problems.

I believe we should not add the "open world" OWL / SNOMED models into the closed world UML, DB, FHIR models for these two different reasons.  OK to put FHIR into RDF or even OWL (after you do all the extra work of making all the disjoint assertions) but keep the connection with the vocabulary the way it is now, via bindings to coded concepts.

Thanks


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From:        "Vipul Kashyap" <kashyap.vipul@gmail.com<mailto:kashyap.vipul@gmail.com>>
To:        Peter Hendler/CA/KAIPERM@KAIPERM
Cc:        <david@dbooth.org<mailto:david@dbooth.org>>, <grahame@healthintersections.com.au<mailto:grahame@healthintersections.com.au>>, <its@lists.hl7.org<mailto:its@lists.hl7.org>>, <lloyd@lmckenzie.com<mailto:lloyd@lmckenzie.com>>, <public-semweb-lifesci@w3.org<mailto:public-semweb-lifesci@w3.org>>, "'Vipul Kashyap'" <kashyap.vipul@gmail.com<mailto:kashyap.vipul@gmail.com>>
Date:        12/20/2014 02:06 PM
Subject:        RE: Minutes of last week's (Dec 2) HL7 ITS RDF Subgroup / W3C HCLS COI call -- Review of FHIR ontology approaches (cont.)
________________________________



Hi Peter,

Thanks for your email below – If I may summarize:

Clinical Models capture the “who, when, where, why”
Snomed/Medical Terminogies – capture the “what”

Agree with your suggestion that Snomed should not be used for the former –
The underlying motivation for my suggestion – as has been suggested by other medical informatics researchers is to
“combine” both information models and terminologies is a common “model/ontology” and leverage the semantic expressiveness of OWL
for the purpose.

I think that primary reason divergence appears to be whether Snomed is viewed as a set of codes which can be used as “tags” or “values”
or Snomed is a full fledged ontology with classes, properties, relationships and instances of those classes. Based on the perspective taken,
Of course there are pros and cons of these approaches and can lead us to different choices of how we model clinical information and knowledge.

---Vipul



From: Peter.Hendler@kp.org<mailto:Peter.Hendler@kp.org> [mailto:Peter.Hendler@kp.org]
Sent: Saturday, December 13, 2014 5:31 PM
To: kashyap.vipul@gmail.com<mailto:kashyap.vipul@gmail.com>
Cc: david@dbooth.org<mailto:david@dbooth.org>; grahame@healthintersections.com.au<mailto:grahame@healthintersections.com.au>; its@lists.hl7.org<mailto:its@lists.hl7.org>; lloyd@lmckenzie.com<mailto:lloyd@lmckenzie.com>; public-semweb-lifesci@w3.org<mailto:public-semweb-lifesci@w3.org>
Subject: RE: Minutes of last week's (Dec 2) HL7 ITS RDF Subgroup / W3C HCLS COI call -- Review of FHIR ontology approaches (cont.)

SNOMED can not and should not map to FHIR resources.  This is the difference between clinical models that capture who, when where and why with the medical terminologies like SNOMED that are only the what.
In HL7 V3, the information model has the entities in roles that participate in acts.  That is perfectly what should be in a clinical model. Then the "what" part of the clinical model may go only as far as say it is an "observation".
SNOMED does not, and should not ever deal with who when where or why.  It only deals with what.

The medical terminology such as SNOMED supplies the "value" of the Observation.  Which might be "diabetes".

There is no one to one between a FHIR observation and a SNOMED concept. They don't overlap. The FHIR, just like the HL7 V3 tells you who when where why but the what stops at "observation". The medical terminology which is linked to that observation resource then can be SNOMED diabetes.  You would not make a FHIR resource for Diabetes. You use the FHIR observation and then code it with a SNOMED value.

The FHIR Observation does not get subclassed to Diabetes.  It is only ever Observaiton.  The specific "value" of the Observation is the medical terminology part supplied for example by SNOMED.

So I would never see it being appropriate to create any SNOMED terms to represent FHIR resources.

Thanks



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From:        "Vipul Kashyap" <kashyap.vipul@gmail.com<mailto:kashyap.vipul@gmail.com>>
To:        "'Grahame Grieve'" <grahame@healthintersections.com.au<mailto:grahame@healthintersections.com.au>>, "'Lloyd McKenzie'" <lloyd@lmckenzie.com<mailto:lloyd@lmckenzie.com>>
Cc:        "'David Booth'" <david@dbooth.org<mailto:david@dbooth.org>>, "'w3c semweb HCLS'" <public-semweb-lifesci@w3.org<mailto:public-semweb-lifesci@w3.org>>, "'HL7 ITS'" <its@lists.hl7.org<mailto:its@lists.hl7.org>>
Date:        12/13/2014 10:41 AM
Subject:        RE: Minutes of last week's (Dec 2) HL7 ITS RDF Subgroup / W3C HCLS COI call -- Review of FHIR ontology approaches (cont.)

________________________________





If every FHIR element was mapped to a snomed term, then you could represent that in RDF no problems.

VK> Would propose that FHIR could be the hub – and we could leverage RDF/OWL constructs to map FHIR elements to Snomed, MedDRA, ICD11, RxNorm, etc.?

However the problem with this is that we already have a slot for mapping an element to it's snomed code, but there are hardly any snomed codes that are appropriate.

VK> Not sure if I understand this – If no Snomed codes are appropriate for a particular FHIR element – then we can request the IHTSDO folks to create a new one, no?
       Also, if the RDF/OWL metamodel gives us the language to express more general relationships – we may not want to use a specific slot for a Snomed code? Or we can perhaps
      Create an axiom linking the values of the snomed code based on the sameAs/subClassOf relationship for a particular terminology, e.g., Snomed?

Thanks,

---Vipul

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Received on Sunday, 21 December 2014 16:34:57 UTC

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