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Re: Agenda GRDDL WG Meeting Jan 31st 11:00 ET

From: Chimezie Ogbuji <ogbujic@bio.ri.ccf.org>
Date: Wed, 31 Jan 2007 01:18:42 -0500 (EST)
To: Harry Halpin <hhalpin@ibiblio.org>
cc: public-grddl-wg <public-grddl-wg@w3.org>
Message-ID: <Pine.GSO.4.60.0701310110470.4659@joplin.bio.ri.ccf.org>

> GRDDL WG Weekly
>          + ACTION: Chime to work on details of 2 allowed results of
>            xinclude test
>    7. Primer Document
>          + ACTION: Chime to propose some primer text for the hl7 case
>          + ACTION: Chime add HL7 plain XML health care to the test
>            suite. See his [12]message


I finally got around to this:

GRDDL XML Usecase

This section uses HL7 CDA as an example of how an XML dialect can be 
gleaned for expressive RDF, satisfying the Health Care: Querying [1] 
XML-based clinical data using an standard ontology usecase. Kayode wants 
to write software components which can extract RDF descriptions from HL7 
CDA documents transmitted from various devices in a healthcare system 
using a clinical ontology with sound ontological commitment.


CDA is a very well-designed information model and heavily optimized for 
messaging between computerized hospital systems:


> the CDA makes documents both machine-readable (so they are easily parsed 
and processed electronically) and human-readable so they can be easily 
retrieved and used by the people who need them. CDA documents can be 
displayed using XML-aware Web browsers or wireless applications such as 
cell phones...


A sample [2] CDA document is included which demonstrates the use of 
expressive clinical coding systems which can be processed by an XSLT 
pipeline resulting in RDF that expresses clinical content in expressive, 
heavily deployed consensus vocabularies such as Open GALEN, DOLCE: 
Descriptive Ontology of Linguistics and Cognitive Engineering, FOAF, and 
an OWL translation of HL7 RIM [4].  An experimental OWL ontology [5] for 
describing basic concepts in a medical record is also used.

Below is a section which describes the author of a ClinicalDocument (a 
cpr:patient-record) and the patient the document is about (foaf:Person / 
cpr:person)

<ClinicalDocument xmlns:grddl='http://www.w3.org/2003/g/data-view#' 
xmlns="urn:hl7-org:v3" grddl:transformation="glean-HL7-CDA.xslt"
   <author>
 	<time value="20000407"/>
 	<assignedAuthor>
 	<id extension="KP00017" root="2.16.840.1.113883.3.933"/>
 	<assignedPerson>
 		<name>
 	    	<given>Robert</given>

 		<family>Dolin</family>
 		<suffix>MD</suffix>
 		</name>
 	</assignedPerson>
         <recordTarget>
 		<patientRole>
 			<patientPatient>
 				<name>
 					<given>Henry</given>
 					<family>Levin</family>
 					<suffix>the 7th</suffix>
 				</name>
 				<administrativeGenderCode code="M" codeSystem="2.16.840.1.113883.5.1"/>
 				<birthTime value="19320924"/>
 			</patientPatient>
 		</patientRole>
 	</recordTarget>
   </author>
</ClinicalDocument>


The following is a set of corresponding RDF statements (expressed in N3 / 
Turtle for brevity and readability) generated from the ClinicalDocument 
'message':

[ a cpr:patient-record ] foaf:maker [ a foaf:Person;
                                         foaf:givenname "Robert";
                                         foaf:family_name "Dolin" ];

                    edns:about [ a cpr:patient; foaf:family_name "Levin";foaf:firstName "Henry" ].


DOLCE, a much more philosophically-oriented ontology describes the about 
relation as:

The relation between information objects and entities they are about.


Much more interesting is an interpretation of a Chest X-ray (a 
cyc:XRayImage or foaf:Image ) which concludes a medical problem 
(cpr:medical-problem).  A SNOMED CT code is used which corresponds to a 
specific term in the Description Logic inspired language which SNOMED CT 
[5] is expressed in.  This mimizes the semantic ambiguity of the exchanged 
message.

<entry xmlns:grddl="http://www.w3.org/2003/g/data-view#" 
grddl:transformation="glean-HL7-CDA.xslt">
 	<Observation>
 	<id root="10.23.4573.15877"/>
 	<code code="282290005" codeSystem="2.16.840.1.113883.6.96" codeSystemName="SNOMED CT" displayName="Imaging interpretation"/>
 	<value xsi:type="CD" code="249674001" codeSystem="2.16.840.1.113883.6.96" codeSystemName="SNOMED CT" displayName="Chest hyperinflated"/>
 	<reference typeCode="SPRT">
 		<ExternalObservation classCode="DGIMG">
 			<id root="123.456.2557"/>
 			<code code="56350004" codeSystem="2.16.840.1.113883.6.96" codeSystemName="SNOMED CT" displayName="Chest-X-ray"/>
 		</ExternalObservation>
 	</reference>
</Observation>

Using a set of vocabulary terms [3] which are expressive about 
interpretations of this kind, equivalent RDF can be extracted.  In 
addition, SKOS terms can be used to express preferred, human readable 
labels

     [ skos:prefLabel "Chest X-ray"; a foaf:Image ]
          foaf:depicts
              [ a cpr:medical-problem;
                skos:prefLabel "Chest hyperinflated" ]

Finally, a procedure is described as having happened at a specific time.

<entry xmlns:grddl="http://www.w3.org/2003/g/data-view#">
 	<Procedure>
 		<code code="30549001" codeSystem="2.16.840.1.113883.6.96" codeSystemName="SNOMED CT" displayName="Suture removal"/>
 		<effectiveTime value="200004071430"/>
 		<targetSiteCode code="66480008" codeSystem="2.16.840.1.113883.6.96" codeSystemName="SNOMED CT" displayName="Left forearm"/>
 	</Procedure>
</entry>

And

         [ a cpr:clinical-description;
                  cpr:description-of [ a rim:ActProcedure;
                          galen:hasSpecificLocation "Left forearm";
                          skos:prefLabel "Suture removal";
                          dc:date "2000-04-07T14:30:00"^^<http://www.w3.org/2001/XMLSchema#dateTime>]]

In each case, a glean:transform attribute is explicitely needed at the 
root of the docment in order for a GRDDL-aware agent to deterministically 
interpret an HL7 CDA message transmitted over the wire.

[1] Note the 'an' was edited from how it is in the usecase document
[2] http://xml.coverpages.org/CDA-ReleaseTwoSample200403.xml
[3] http://esw.w3.org/topic/HCLS/OntologyTaskForce/POMR?action=AttachFile&do=get&target=POMR-slides.html#(7)
[4] http://esw.w3.org/topic/HCLS/ACPPTaskForce?action=AttachFile&do=get&target=RIMV3OWL.zip
[5] http://www.snomed.org/snomedct/index.html


Chimezie Ogbuji
Lead Systems Analyst
Thoracic and Cardiovascular Surgery
Cleveland Clinic Foundation
9500 Euclid Avenue/ W26
Cleveland, Ohio 44195
Office: (216)444-8593
ogbujic@ccf.org
Received on Wednesday, 31 January 2007 06:18:49 GMT

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