Semantic Interpretation of Health Care Data

SemTech
7 May, 2013

Eric Prud'hommeaux, <eric@w3.org>
- Sanitation Engineer, W3C

Agenda

Patient visit
Notional graph
RIM graph
BRIDG graph

Recordable Clinical Data

encounter
allergies
immunizations
history
demographics
vitals
problem statement

labs
diagnosis
prescription
treatment plan
procedure
adverse events
outcome

inclusion/exclusion criteria

protocol deviations

Procedure

On Jan 25, 2013, Isabella Jones got an Influenza Virus vaccine from Dr. Henry Seven at 1002 Healthcare Dr Beaverton OR. He's acting on behalf of NEXTGEN Medical Practice (Horsham) of Horsham PA.

Simple (Naive) Graph

clinic:encounter1 a ont:Encounter ;
    ont:date "2013-01-25"^^xsd:date ;
    ont:patient clinic:Patient003 ;
    ont:act [ a ont:Physical … ], [
        a ont:Vaccination, ont:InfluenzaVirusVaccine ;
        ont:performer clinic:dr005 ;
    ] ;
    ont:location [
        a ont:Address ;
        ont:streetNo 1002 ; ont:streetName "Healthcare Dr." ;
        ont:city "Beaverton" ; ont:stateCode "OR"
    ] ;
    ont:practice clinic:NextGen .

clinic:Patient003 a ont:Patient ;
    ont:givenName "Isabella" ; ont:familyName "Jones" ;
    ont:insurance … .

clinic:dr005 a ont:Physician ;
    ont:givenName "Henry" ; ont:familyName "Seven" ;
    ont:practiceNumber 123456 .

clinic:NextGen a ont:Clinic ;
    ont:name "NEXTGEN Medical Practice (Horsham)" ;
    ont:location [ … ] .

Coding Systems

clinic:encounter1 a ont:Encounter ;
    ont:date "2013-01-25"^^xsd:date ;
    ont:patient clinic:Patient003 ;
    ont:act [ a ont:Physical … ], [
        a ont:Vaccination , ont:InfluenzaVirusVaccine ;
	ont:code [
            ont:code 2670 ; ont:codeSystem="2.16.840.1.113883.6.88" ;
            ont:displayName="Codeine" ; ont:codeSystemName="RxNorm"
        ] ;
        ont:performer clinic:dr005 ;
    ] ;
    ont:location [
        a ont:Address ;
        ont:streetNo 1002 ; ont:streetName "Healthcare Dr." ;
        ont:city "Beaverton" ; ont:stateCode "OR"
    ] ;
    ont:practice clinic:NextGen .

clinic:Patient003 a ont:Patient ;
    ont:givenName "Isabella" ; ont:familyName "Jones" ;
    ont:insurance … .

clinic:dr005 a ont:Physician ;
    ont:givenName "Henry" ; ont:familyName "Seven" ;
    ont:practiceNumber 123456 .

clinic:NextGen a ont:Clinic ;
    ont:name "NEXTGEN Medical Practice (Horsham)" ;
    ont:location [ … ] .

= Terminological Model

Structural Relationships

clinic:encounter1 a ont:Encounter ;
    ont:date "2013-01-25"^^xsd:date ;
    ont:patient clinic:Patient003 ;
    ont:act [ a ont:Physical … ], [
        a ont:Vaccination ;
	ont:code [
            ont:code 2670 ; ont:codeSystem="2.16.840.1.113883.6.88" ;
            ont:displayName="Codeine" ; ont:codeSystemName="RxNorm"
        ] ;
        ont:performer clinic:dr005 ;
    ] ;
    ont:location [
        a ont:Address ;
        ont:streetNo 1002 ; ont:streetName "Healthcare Dr." ;
        ont:city "Beaverton" ; ont:stateCode "OR"
    ] ;
    ont:practice clinic:NextGen .

clinic:Patient003 a ont:Patient ;
    ont:givenName "Isabella" ; ont:familyName "Jones" ;
    ont:insurance … .

clinic:dr005 a ont:Physician ;
    ont:givenName "Henry" ; ont:familyName "Seven" ;
    ont:practiceNumber 123456 .

clinic:NextGen a ont:Clinic ;
    ont:name "NEXTGEN Medical Practice (Horsham)" ;
    ont:location [ … ] .

= Information Model

Clinical Trials Input

	    <entry typeCode="DRIV">
	      <procedure classCode="PROC" moodCode="EVN">
		<templateId root="2.16.840.1.113883.10.20.22.4.14"/>
		<id root="2.201" extension="8e4b2fcb-13e8-4ce6-8737-61c3c9c328ec"/>
		<code nullFlavor="OTH">
		  <originalText>
		    <reference value="#ProcedureDescription_0"/>
		  </originalText>
		  <translation code="90732" displayName="Immunization admin, 1 vaccine" codeSystem="2.16.840.1.113883.6.12" codeSystemName="CPT4" xsi:type="CE"/>
		</code>
		<statusCode code="completed"/>
		<effectiveTime>
		  <low value="20130125"/>
		  <high value="20130125"/>
		</effectiveTime>
		<entryRelationship typeCode="COMP" inversionInd="true">
	      <encounter classCode="ENC" moodCode="EVN">
		<templateId root="2.16.840.1.113883.10.20.22.4.49"/>
		<id root="2.201" extension="a778b36c-2a08-4f41-bc2a-3f29293c4e3c"/>
		<code nullFlavor="UNK">
		  <originalText>
		    <reference value="#Encounter_0"/>
		  </originalText>
		</code>
		<text>
		  <reference value="#Encounter_0"/>
		</text>
		<effectiveTime>
		  <low value="20120806"/>
		  <high value="20120806"/>
		</effectiveTime>
		<performer>
		  <assignedEntity classCode="ASSIGNED">
		    <id extension="e163b5c3-83a9-4937-b0e4-ce773eb3f8e4" root="2.201"/>
		    <addr>
		      <streetAddressLine>1002 Healthcare Dr</streetAddressLine>
		      <city>Beaverton</city>
		      <state>OR</state>
		      <postalCode>97005</postalCode>
		      <country nullFlavor="UNK"/>
		    </addr>
		    <telecom use="WP" value="tel:+1-5555551002"/>
		    <assignedPerson>
		      <name>
			<family>Seven</family>
			<given>Henry</given>
			<given>L</given>
		      </name>
		    </assignedPerson>
		    <representedOrganization>
		      <id root="2.201" extension="0001"/>
		      <id root="2.16.840.1.113883.4.6" extension="1234567893"/>
		      <name>NEXTGEN Medical Practice (Horsham)</name>
		      <telecom use="WP" value="tel:+1-2156577010"/>
		      <addr>
			<streetAddressLine>795 Horsham Road</streetAddressLine>
			<city>Horsham</city>
			<state>PA</state>
			<postalCode>19044</postalCode>
		      </addr>
		    </representedOrganization>
		  </assignedEntity>
		</performer>
		<participant typeCode="LOC">
		  <participantRole classCode="SDLOC">
		    <templateId root="2.16.840.1.113883.10.20.22.4.32"/>
		    <id extension="635dc59b-e421-4aeb-9cc8-11c36cf1d6ed" root="2.201"/>
		    <code nullFlavor="UNK"/>
		    <addr>
		      <streetAddressLine>1002 Healthcare Dr</streetAddressLine>
		      <city>Beaverton</city>
		      <state>OR</state>
		      <postalCode>97005</postalCode>
		    </addr>
		    <telecom use="WP" nullFlavor="UNK"/>
		    <playingEntity classCode="PLC">
		      <name>Get Well Clinic</name>
		    </playingEntity>
		  </participantRole>
		</participant>
		<entryRelationship typeCode="RSON">
		  <observation classCode="OBS" moodCode="EVN">
		    <templateId root="2.16.840.1.113883.10.20.22.4.19"/>
		    <id nullFlavor="NA"/>
		    <code code="409586006" displayName="Complaint" codeSystem="2.16.840.1.113883.6.96" codeSystemName="SNOMED CT"/>
		    <statusCode code="completed"/>
		    <effectiveTime value="20130125"/>
		    <value nullFlavor="UNK" xsi:type="CD">
		      <originalText>
			<reference value="#Encounter_0"/>
		      </originalText>
		    </value>
		  </observation>
		</entryRelationship>
		<entryRelationship typeCode="SUBJ">
		  <act classCode="ACT" moodCode="EVN">
		    <templateId root="2.16.840.1.113883.10.20.22.4.80"/>
		    <code code="29308-4" displayName="Diagnosis" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC" xsi:type="CE"/>
		    <entryRelationship typeCode="SUBJ">
		      <observation classCode="OBS" moodCode="EVN">
			<templateId root="2.16.840.1.113883.10.20.22.4.4"/>
			<id nullFlavor="UNK"/>
			<code code="282291009" displayName="Diagnosis" codeSystem="2.16.840.1.113883.6.96" codeSystemName="SNOMED CT"/>
			<statusCode code="completed"/>
			<effectiveTime>
			  <low value="20130125"/>
			</effectiveTime>
			<value nullFlavor="OTH" xsi:type="CD">
			  <translation code="799.02" displayName="Hypoxemia" codeSystem="2.16.840.1.113883.6.103" codeSystemName="ICD-9-CM"/>
			</value>
		      </observation>
		    </entryRelationship>
		  </act>
		</entryRelationship>
		<entryRelationship typeCode="SUBJ">
		  <act classCode="ACT" moodCode="EVN">
		    <templateId root="2.16.840.1.113883.10.20.22.4.80"/>
		    <code code="29308-4" displayName="Diagnosis" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC" xsi:type="CE"/>
		    <entryRelationship typeCode="SUBJ">
		      <observation classCode="OBS" moodCode="EVN">
			<templateId root="2.16.840.1.113883.10.20.22.4.4"/>
			<id nullFlavor="UNK"/>
			<code code="282291009" displayName="Diagnosis" codeSystem="2.16.840.1.113883.6.96" codeSystemName="SNOMED CT"/>
			<statusCode code="completed"/>
			<effectiveTime>
			  <low value="20130125"/>
			</effectiveTime>
			<value nullFlavor="OTH" xsi:type="CD">
			  <translation code="486" displayName="Community acquired pneumonia" codeSystem="2.16.840.1.113883.6.103" codeSystemName="ICD-9-CM"/>
			</value>
		      </observation>
		    </entryRelationship>
		  </act>
		</entryRelationship>
		<entryRelationship typeCode="SUBJ">
		  <act classCode="ACT" moodCode="EVN">
		    <templateId root="2.16.840.1.113883.10.20.22.4.80"/>
		    <code code="29308-4" displayName="Diagnosis" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC" xsi:type="CE"/>
		    <entryRelationship typeCode="SUBJ">
		      <observation classCode="OBS" moodCode="EVN">
			<templateId root="2.16.840.1.113883.10.20.22.4.4"/>
			<id nullFlavor="UNK"/>
			<code code="282291009" displayName="Diagnosis" codeSystem="2.16.840.1.113883.6.96" codeSystemName="SNOMED CT"/>
			<statusCode code="completed"/>
			<effectiveTime>
			  <low value="20130125"/>
			</effectiveTime>
			<value nullFlavor="OTH" xsi:type="CD">
			  <translation code="493.90" displayName="Asthma" codeSystem="2.16.840.1.113883.6.103" codeSystemName="ICD-9-CM"/>
			</value>
		      </observation>
		    </entryRelationship>
		  </act>
		</entryRelationship>
	      </encounter>
		  <!--encounter classCode="ENC" moodCode="EVN">
		    <id extension="a778b36c-2a08-4f41-bc2a-3f29293c4e3c" root="2.201"/>
		    <code nullFlavor="UNK"/>
		  </encounter -->
		</entryRelationship>
	      </procedure>
	    </entry>

O-RIM

Take heart, there is a semantic representation of this data.

Immunization in Turtle

see the html-ized Turtle, and C-CDA RMIM.

[ a rim:ActRelationship ;
    rim:ActRelationship.typeCode [ dt:CD.code "DRIV" ; dt:CD.codeSystem "???" ] ;
    rim:ActRelationship.source _:section8 ;
    rim:ActRelationship.target _:section8_immunizationActivity0
] .
_:section8_immunizationActivity0 a rim:Act ;
    rim:Act.id [ a dt:DSET_II ;
        dt:COLL.item [ dt:II.root "45d0cab8-881c-43e5-84e6-450a16fed1b7" ]
    ] ;
    rim:Act.classCode [ dt:CD.code "SBADM" ; dt:CD.codeSystem "???" ] ;
    rim:Act.moodCode [ dt:CD.code "EVN" ; dt:CD.codeSystem "2.16.840.1.113883.5.1001" ] ;
    rim:Act.effectiveTime "2012-08-06"^^xsd:date ;
    rim:Act.statusCode "completed" ;
  
    rim:Act.code [
        dt:CD.code "IMMUNIZ" ; dt:CD.codeSystem "2.16.840.1.113883.5.4" ;
        dt:CD.codeSystemName "ActCode"
    ]
# Consumable ManufacturedMaterial
[ a rim:Participation ;
    rim:Participation.typeCode [ dt:CD.code "CSM" ; dt:CD.codeSystem "???" ] ;
    rim:Participation.act _:section8_immunizationActivity0 ;
    rim:Participation.role _:section8_immunizationActivity0_consumable0
] .
_:section8_immunizationActivity0_consumable0 a rim:Role ;

    rim:Role.player _:section8_immunizationActivity0_consumable0_player ;
    rim:Role.classCode [ dt:CD.code "MANU" ; dt:CD.codeSystem "???" ] ;
.
_:section8_immunizationActivity0_consumable0_player a rim:ManufacturedMaterial ;
    rim:Entity.classCode [ dt:CD.code "MMAT" ; dt:CD.codeSystem "???" ] ;
    # rim:Entity.determinerCode [ dt:CD.code "???" ; dt:CD.codeSystem "???" ] ;
    rim:Entity.code [
        dt:CD.code "33" ; dt:CD.codeSystem "2.16.840.1.113883.12.292" ;
        dt:CD.displayName "Pneumo (2 yrs or older) (PPV23)" ; dt:CD.codeSystemName "CVX"
    ];
    rim:ManufacturedMaterial.lotNumberText [ dt:ED.value "90390" ] ;
    # rim:ManufacturedMaterial.manufacturerOrganization "GlaxoSmithKline"

.

# Performer Participation
[ a rim:Participation ;
    rim:Participation.typeCode [ dt:CD.code "PRF" ; dt:CD.codeSystem "???" ] ;
    rim:Participation.act _:section8_immunizationActivity0 ;
    rim:Participation.role _:section8_immunizationActivity0_performer0
] .
_:section8_immunizationActivity0_performer0 a rim:Role ;
    rim:Role.id [ a dt:DSET_II ;
        dt:COLL.item [ dt:II.root "2.401" ; dt:II.extension "f3fdfa1a-6d4b-4ecd-889b-fe6e7798425e" ]
    ] ;
    rim:Role.player _:section8_immunizationActivity0_performer0_player ;
    rim:Role.classCode [ dt:CD.code "ASSIGNED" ; dt:CD.codeSystem "???" ] ;
    rim:Role.telecom [ a dt:COLL_TEL ; dt:CD.code "UNK" ; dt:CD.codeSystem "@@HL7 UNK code system" ];
    rim:Role.addr [ a dt:COLL_AD ;

    ] ;
.
_:section8_immunizationActivity0_performer0_player a rim:Person ;
    rim:Entity.classCode [ dt:CD.code "PSN" ; dt:CD.codeSystem "???" ] ;
    rim:Entity.determinerCode [ dt:CD.code "INSTANCE" ; dt:CD.codeSystem "???" ] ;
    # rim:Entity.code ???
    rim:Entity.name [ a dt:COLL_EN ;
        # dt:COLL.item [ x:person-name-family "Villalon RN" ] ;
        # dt:COLL.item [ x:person-name-given "May" ] ;
    ];
 ;

 ;


.

# SUBJ
[ a rim:ActRelationship ;
    rim:ActRelationship.typeCode [ dt:CD.code "REFR" ; dt:CD.codeSystem "???" ] ;
    rim:ActRelationship.source _:section8_immunizationActivity0 ;
    rim:ActRelationship.target _:section8_immunizationActivity0_entryRelationship0
] .
_:section8_immunizationActivity0_entryRelationship0 a rim:Observation ;

    rim:Act.classCode [ dt:CD.code "OBS" ; dt:CD.codeSystem "2.16.840.1.113883.5.6" ] ;
    rim:Act.moodCode [ dt:CD.code "EVN" ; dt:CD.codeSystem "2.16.840.1.113883.5.1001" ] ;
    rim:Act.statusCode "completed" ;
  
    rim:Act.code [
        dt:CD.code "30973-2" ; dt:CD.codeSystem "2.16.840.1.113883.6.1" ;
        dt:CD.displayName "DOSE NUMBER" ; dt:CD.codeSystemName "LOINC"
    ];
    rim:Observation.value [ a dt:PQ ; # unknown units 
        dt:PQ.value [ a dt:REAL ; dt:value "999" ] 
    ] ;;.
# SUBJ
[ a rim:ActRelationship ;
    rim:ActRelationship.typeCode [ dt:CD.code "REFR" ; dt:CD.codeSystem "???" ] ;
    rim:ActRelationship.source _:section8_immunizationActivity0 ;
    rim:ActRelationship.target _:section8_immunizationActivity0_entryRelationship1
] .
_:section8_immunizationActivity0_entryRelationship1 a rim:Act ;

    rim:Act.classCode [ dt:CD.code "ACT" ; dt:CD.codeSystem "2.16.840.1.113883.5.6" ] ;
    rim:Act.moodCode [ dt:CD.code "EVN" ; dt:CD.codeSystem "2.16.840.1.113883.5.1001" ] ;
    rim:Act.statusCode "completed" ;
  
    rim:Act.code [
        dt:CD.code "48767-8" ; dt:CD.codeSystem "2.16.840.1.113883.6.1" ;
        dt:CD.displayName "ANNOTATION COMMENT" ; dt:CD.codeSystemName "LOINC"
    ];.
# REFR
[ a rim:ActRelationship ;
    rim:ActRelationship.typeCode [ dt:CD.code "REFR" ; dt:CD.codeSystem "???" ] ;
    rim:ActRelationship.source _:section8_immunizationActivity0 ;
    rim:ActRelationship.target _:section8_immunizationActivity0_entryRelationship2
] .
_:section8_immunizationActivity0_entryRelationship2 a rim:Observation ;

    rim:Act.classCode [ dt:CD.code "OBS" ; dt:CD.codeSystem "2.16.840.1.113883.5.6" ] ;
    rim:Act.moodCode [ dt:CD.code "EVN" ; dt:CD.codeSystem "2.16.840.1.113883.5.1001" ] ;
    rim:Act.statusCode "completed" ;
  
    rim:Act.code [
        dt:CD.code "33999-4" ; dt:CD.codeSystem "2.16.840.1.113883.6.1" ;
        dt:CD.displayName "STATUS" ; dt:CD.codeSystemName "LOINC"
    ];
    rim:Observation.value [ a dt:PQ ;
        dt:CD.code [ a dt:CD ;
            rim:CD.code "39252100" ; rim:CD.codeSystem "2.16.840.1.113883.6.96" ;
            rim:CD.displayName "Prior History" ; rim:CD.codeSystemName "SNOMED CT"
        ] 
    ] ;;.
# REFR
[ a rim:ActRelationship ;
    rim:ActRelationship.typeCode [ dt:CD.code "REFR" ; dt:CD.codeSystem "???" ] ;
    rim:ActRelationship.source _:section8_immunizationActivity0 ;
    rim:ActRelationship.target _:section8_immunizationActivity0_entryRelationship3
] .
_:section8_immunizationActivity0_entryRelationship3 a rim:Act ;
    rim:Act.id [ a dt:DSET_II ;
        dt:COLL.item [ dt:II.root "2.201" ; dt:II.extension "a778b36c-2a08-4f41-bc2a-3f29293c4e3c" ]
    ] ;
    rim:Act.classCode [ dt:CD.code "ACT" ; dt:CD.codeSystem "2.16.840.1.113883.5.6" ] ;
    rim:Act.moodCode [ dt:CD.code "EVN" ; dt:CD.codeSystem "2.16.840.1.113883.5.1001" ] ;
    rim:Act.code [
        dt:CD.code "UNK" ; dt:CD.codeSystem "@@HL7 UNK code system" ;
        dt:CD.displayName "@@beats me" ; dt:CD.codeSystemName "@@HL7"
    ];.
;
    rim:SubstanceAdministration.doseQuantity [ a dt:PQ ; # unknown units 
        dt:PQ.value [
            dt:CD.code "UNK" ; dt:CD.codeSystem "@@HL7 UNK code system" ;
            dt:CD.displayName "@@beats me" ; dt:CD.codeSystemName "@@HL7"
        ] 
    ] ;.

# Consumable ManufacturedMaterial
[ a rim:Participation ;
    rim:Participation.typeCode [ dt:CD.code "CSM" ; dt:CD.codeSystem "???" ] ;
    rim:Participation.act _:section8_immunizationActivity0 ;
    rim:Participation.role _:section8_immunizationActivity0_consumable0
] .
_:section8_immunizationActivity0_consumable0 a rim:Role ;

    rim:Role.player _:section8_immunizationActivity0_consumable0_player ;
    rim:Role.classCode [ dt:CD.code "MANU" ; dt:CD.codeSystem "???" ] ;
.
_:section8_immunizationActivity0_consumable0_player a rim:ManufacturedMaterial ;
    rim:Entity.classCode [ dt:CD.code "MMAT" ; dt:CD.codeSystem "???" ] ;
    # rim:Entity.determinerCode [ dt:CD.code "???" ; dt:CD.codeSystem "???" ] ;
    rim:Entity.code [
        dt:CD.code "33" ; dt:CD.codeSystem "2.16.840.1.113883.12.292" ;
        dt:CD.displayName "Pneumo (2 yrs or older) (PPV23)" ; dt:CD.codeSystemName "CVX"
    ];
    rim:ManufacturedMaterial.lotNumberText [ dt:ED.value "90390" ] ;
    # rim:ManufacturedMaterial.manufacturerOrganization "GlaxoSmithKline"

.

# Performer Participation
[ a rim:Participation ;
    rim:Participation.typeCode [ dt:CD.code "PRF" ; dt:CD.codeSystem "???" ] ;
    rim:Participation.act _:section8_immunizationActivity0 ;
    rim:Participation.role _:section8_immunizationActivity0_performer0
] .
_:section8_immunizationActivity0_performer0 a rim:Role ;
    rim:Role.id [ a dt:DSET_II ;
        dt:COLL.item [ dt:II.root "2.401" ; dt:II.extension "f3fdfa1a-6d4b-4ecd-889b-fe6e7798425e" ]
    ] ;
    rim:Role.player _:section8_immunizationActivity0_performer0_player ;
    rim:Role.classCode [ dt:CD.code "ASSIGNED" ; dt:CD.codeSystem "???" ] ;
    rim:Role.telecom [ a dt:COLL_TEL ; dt:CD.code "UNK" ; dt:CD.codeSystem "@@HL7 UNK code system" ];
    rim:Role.addr [ a dt:COLL_AD ;

    ] ;
.
_:section8_immunizationActivity0_performer0_player a rim:Person ;
    rim:Entity.classCode [ dt:CD.code "PSN" ; dt:CD.codeSystem "???" ] ;
    rim:Entity.determinerCode [ dt:CD.code "INSTANCE" ; dt:CD.codeSystem "???" ] ;
    # rim:Entity.code ???
    rim:Entity.name [ a dt:COLL_EN ;
        # dt:COLL.item [ x:person-name-family "Villalon RN" ] ;
        # dt:COLL.item [ x:person-name-given "May" ] ;
    ];
 ;

 ;


.

# SUBJ
[ a rim:ActRelationship ;
    rim:ActRelationship.typeCode [ dt:CD.code "REFR" ; dt:CD.codeSystem "???" ] ;
    rim:ActRelationship.source _:section8_immunizationActivity0 ;
    rim:ActRelationship.target _:section8_immunizationActivity0_entryRelationship0
] .
_:section8_immunizationActivity0_entryRelationship0 a rim:Observation ;

    rim:Act.classCode [ dt:CD.code "OBS" ; dt:CD.codeSystem "2.16.840.1.113883.5.6" ] ;
    rim:Act.moodCode [ dt:CD.code "EVN" ; dt:CD.codeSystem "2.16.840.1.113883.5.1001" ] ;
    rim:Act.statusCode "completed" ;
  
    rim:Act.code [
        dt:CD.code "30973-2" ; dt:CD.codeSystem "2.16.840.1.113883.6.1" ;
        dt:CD.displayName "DOSE NUMBER" ; dt:CD.codeSystemName "LOINC"
    ];
    rim:Observation.value [ a dt:PQ ; # unknown units 
        dt:PQ.value [ a dt:REAL ; dt:value "999" ] 
    ] ;;.
# SUBJ
[ a rim:ActRelationship ;
    rim:ActRelationship.typeCode [ dt:CD.code "REFR" ; dt:CD.codeSystem "???" ] ;
    rim:ActRelationship.source _:section8_immunizationActivity0 ;
    rim:ActRelationship.target _:section8_immunizationActivity0_entryRelationship1
] .
_:section8_immunizationActivity0_entryRelationship1 a rim:Act ;

    rim:Act.classCode [ dt:CD.code "ACT" ; dt:CD.codeSystem "2.16.840.1.113883.5.6" ] ;
    rim:Act.moodCode [ dt:CD.code "EVN" ; dt:CD.codeSystem "2.16.840.1.113883.5.1001" ] ;
    rim:Act.statusCode "completed" ;
  
    rim:Act.code [
        dt:CD.code "48767-8" ; dt:CD.codeSystem "2.16.840.1.113883.6.1" ;
        dt:CD.displayName "ANNOTATION COMMENT" ; dt:CD.codeSystemName "LOINC"
    ];.
# REFR
[ a rim:ActRelationship ;
    rim:ActRelationship.typeCode [ dt:CD.code "REFR" ; dt:CD.codeSystem "???" ] ;
    rim:ActRelationship.source _:section8_immunizationActivity0 ;
    rim:ActRelationship.target _:section8_immunizationActivity0_entryRelationship2
] .
_:section8_immunizationActivity0_entryRelationship2 a rim:Observation ;

    rim:Act.classCode [ dt:CD.code "OBS" ; dt:CD.codeSystem "2.16.840.1.113883.5.6" ] ;
    rim:Act.moodCode [ dt:CD.code "EVN" ; dt:CD.codeSystem "2.16.840.1.113883.5.1001" ] ;
    rim:Act.statusCode "completed" ;
  
    rim:Act.code [
        dt:CD.code "33999-4" ; dt:CD.codeSystem "2.16.840.1.113883.6.1" ;
        dt:CD.displayName "STATUS" ; dt:CD.codeSystemName "LOINC"
    ];
    rim:Observation.value [ a dt:PQ ;
        dt:CD.code [ a dt:CD ;
            rim:CD.code "39252100" ; rim:CD.codeSystem "2.16.840.1.113883.6.96" ;
            rim:CD.displayName "Prior History" ; rim:CD.codeSystemName "SNOMED CT"
        ] 
    ] ;;.
# REFR
[ a rim:ActRelationship ;
    rim:ActRelationship.typeCode [ dt:CD.code "REFR" ; dt:CD.codeSystem "???" ] ;
    rim:ActRelationship.source _:section8_immunizationActivity0 ;
    rim:ActRelationship.target _:section8_immunizationActivity0_entryRelationship3
] .
_:section8_immunizationActivity0_entryRelationship3 a rim:Act ;
    rim:Act.id [ a dt:DSET_II ;
        dt:COLL.item [ dt:II.root "2.201" ; dt:II.extension "a778b36c-2a08-4f41-bc2a-3f29293c4e3c" ]
    ] ;
    rim:Act.classCode [ dt:CD.code "ACT" ; dt:CD.codeSystem "2.16.840.1.113883.5.6" ] ;
    rim:Act.moodCode [ dt:CD.code "EVN" ; dt:CD.codeSystem "2.16.840.1.113883.5.1001" ] ;
    rim:Act.code [
        dt:CD.code "UNK" ; dt:CD.codeSystem "@@HL7 UNK code system" ;
        dt:CD.displayName "@@beats me" ; dt:CD.codeSystemName "@@HL7"
    ];.

predicates as classCodes

see the html-ized Turtle, and C-CDA RMIM.

[ a rim:ActRelationship ;
    rim:ActRelationship.typeCode [ dt:CD.code "DRIV" ; dt:CD.codeSystem "???" ] ;
    rim:ActRelationship.source _:section8 ;
    rim:ActRelationship.target _:section8_immunizationActivity0
] .
_:section8_immunizationActivity0 a rim:Act ;
    rim:Act.id [ a dt:DSET_II ;
        dt:COLL.item [ dt:II.root "45d0cab8-881c-43e5-84e6-450a16fed1b7" ]
    ] ;
    rim:Act.classCode [ dt:CD.code "SBADM" ; dt:CD.codeSystem "???" ] ;
    rim:Act.moodCode [ dt:CD.code "EVN" ; dt:CD.codeSystem "2.16.840.1.113883.5.1001" ] ;
    rim:Act.effectiveTime "2012-08-06"^^xsd:date ;
    rim:Act.statusCode "completed" ;
  
    rim:Act.code [
        dt:CD.code "IMMUNIZ" ; dt:CD.codeSystem "2.16.840.1.113883.5.4" ;
        dt:CD.codeSystemName "ActCode"
    ]
# Consumable ManufacturedMaterial
[ a rim:Participation ;
    rim:Participation.typeCode [ dt:CD.code "CSM" ; dt:CD.codeSystem "???" ] ;
    rim:Participation.act _:section8_immunizationActivity0 ;
    rim:Participation.role _:section8_immunizationActivity0_consumable0
] .
_:section8_immunizationActivity0_consumable0 a rim:Role ;

    rim:Role.player _:section8_immunizationActivity0_consumable0_player ;
    rim:Role.classCode [ dt:CD.code "MANU" ; dt:CD.codeSystem "???" ] ;
.
_:section8_immunizationActivity0_consumable0_player a rim:ManufacturedMaterial ;
    rim:Entity.classCode [ dt:CD.code "MMAT" ; dt:CD.codeSystem "???" ] ;
    # rim:Entity.determinerCode [ dt:CD.code "???" ; dt:CD.codeSystem "???" ] ;
    rim:Entity.code [
        dt:CD.code "33" ; dt:CD.codeSystem "2.16.840.1.113883.12.292" ;
        dt:CD.displayName "Pneumo (2 yrs or older) (PPV23)" ; dt:CD.codeSystemName "CVX"
    ];
    rim:ManufacturedMaterial.lotNumberText [ dt:ED.value "90390" ] ;
    # rim:ManufacturedMaterial.manufacturerOrganization "GlaxoSmithKline"

.

Clinical Trials Input

Clinical trials are based on CRFs, composed of carefully vetted questions.
Various terminologies provide viable answers to them.
- Can be precice (simple, comminuted) or generic (1+, 2+, mild, medium) or procedural (not_measured, not/applicable)

3rd parties compose value sets of permissible values.

pharma1:valueSet1234 owl:oneOf (
        terminology1:1Plus  terminology1:2Plus
        terminology1:3Plus  terminology1:4Plus ).

Cross-study metadata analysis requires semantically-tagged questions.
- What studies measured exercise tolerance in the presence of Damitol™?
Cross-study data analysis additionally requires consistent or mapped value sets.
- What do all our studies say about associations between cardio-vascular abnormalities and Viox?

Trial Data Interpretation

Contextual data captured in protocol (not machine-readable)
e.g. post @@ BP administered 10 minutes after administering @@foo.
Data not captured using medical terminologies (e.g. SNOMED).
Off-CRF data is specifically discouraged. (per ICH E3 and E6).

Policy

The European Medicines Agency (EMA) pushing publication of clinical-trial data for public health,
Goal of understandable clinical data formats.
FDA goal of improved use of submitted clinical trial data.
Pharmaceutical companies have attempted to use submission standards to create study repositories.

How's that going?

Around 2009, CDISC members identified a need for intra and inter pharma sharing of trial metadata:

questions
value sets

They were going to call it SHARE.

4 years later,

GSK started their own.
Roche, AZ mapping SDTM to RDF.
Abbvie, Boehringer Ingelheim, AstraZeneca, BMS, GSK, J&J, Lilly, Pfizer, Roche, Sanofi formed TranCelerate.

Data

GSK's patient data.
Lilly's <http://lillytrials.com/>.

RDF-y Schemas/Ontologies

RIM
BRIDG
21090
11179
SNOMED
LOINC
CDISC2RDF's schemas
O-RIM -- grounds BRIDG, C-CDA (to use clinical data for clinical research)

Example: extercise tolerance

Extol has a label of "Exercise Tolerance".

pharma1:Q_Extol rdfs:label "Exercise tolerance"  ;

Extol is a subclass of CRFQuestion and pulmonary_functon_testing

  rdfs:subClassOf prot:CRFQuestion , LOINC:pulmonary_functon_testing ,

every Extol has an obsValue property with a value in valueSet1234.

     [ owl:onProperty prot:obsValue ; owl:allValuesFrom pharma1:valueSet1234 ] .

Example: ...

pharma1:Q_Extol rdfs:label "Exercise tolerance"  ;
  rdfs:subClassOf prot:CRFQuestion , LOINC:pulmonary_functon_testing ,
     [ owl:onProperty prot:obsValue ; owl:allValuesFrom pharma1:valueSet1234 ] .
pharma2:Q_Tread rdfs:label "Treadmill endurance" ;
  rdfs:subClassOf prot:CRFQuestion , LOINC:cardiac_function_testing ,
     [ owl:onProperty prot:obsValue ; owl:allValuesFrom pharma2:valueSetPick ] .
pharma2:Q_Sleep rdfs:label "Sleep disturbance"   ;
  rdfs:subClassOf prot:CRFQuestion , LOINC:interruption_of_REM_sleep ,
     [ owl:onProperty prot:obsValue ; owl:allValuesFrom pharma2:valueSetBoth ] .

Semantic Interpretation of Health Care Data

SemTech 7 May, 2013

Agenda

Recordable Clinical Data

Procedure

Simple (Naive) Graph

Coding Systems

= Terminological Model

Structural Relationships

= Information Model

Clinical Trials Input

O-RIM

Immunization in Turtle

predicates as classCodes

Clinical Trials Input

Trial Data Interpretation

Policy

How's that going?

Data

RDF-y Schemas/Ontologies

Example: extercise tolerance

Example: ...

SemTech
7 May, 2013