hl7 the data standard for biomedical informatics gcrc biomedical informatics workshop october 29-30,...

HL7 The Data Standard for HL7 The Data Standard for Biomedical InformaticsBiomedical Informatics

GCRC Biomedical Informatics WorkshopGCRC Biomedical Informatics Workshop

October 29-30, 2003, Bethesda, MDOctober 29-30, 2003, Bethesda, MD

Gunther Schadow, MD, PhDRegenstrief Institute, IndianaUniversity School of Medicine,Indianapolis, IN

11/10/200211/10/2002 Copyright (c) 1999-2002 Regenstrief Institute for Health CareCopyright (c) 1999-2002 Regenstrief Institute for Health Care 22

What is HL7?What is HL7?

• ANSI accredited Standard Development ANSI accredited Standard Development Organization (SDO) Organization (SDO) to provide standards to provide standards forfor• the exchange, management and integration ofthe exchange, management and integration of

• data that support data that support • clinical patient care and the clinical patient care and the • management, delivery and evaluation of management, delivery and evaluation of

healthcare services. Specifically, tohealthcare services. Specifically, to

• create flexible, cost effective create flexible, cost effective • approaches, standards, guidelines, approaches, standards, guidelines,

methodologies, and related services for methodologies, and related services for

• interoperability between healthcare interoperability between healthcare information systems.information systems.


What HL7 Products Exist?What HL7 Products Exist?• HL7 version 2 messaging standards forHL7 version 2 messaging standards for

• Patient administration, Order Entry, ResultsPatient administration, Order Entry, Results• Medical data “attachments” to HIPAA Medical data “attachments” to HIPAA

transactionstransactions• HL7 version 3 specifications forHL7 version 3 specifications for

• all of the above, plusall of the above, plus• Clinical Document ArchitectureClinical Document Architecture• Reference Information Model (RIM) for Reference Information Model (RIM) for

HealthcareHealthcare• includes Data Type Specification for health careincludes Data Type Specification for health care• XML Data Formats for Medical InformationXML Data Formats for Medical Information• Controlled VocabularyControlled Vocabulary

• Others (by acquisition)Others (by acquisition)• Arden SyntaxArden Syntax• C-COW (clinical desktop integration)C-COW (clinical desktop integration)


Good friends of HL7Good friends of HL7

• Logical Observation Identifiers, Names and Logical Observation Identifiers, Names and Codes (LOINC)Codes (LOINC)• vocabulary of medical observations (laboratory vocabulary of medical observations (laboratory

and clinical)and clinical)• practical developed for and with the industrypractical developed for and with the industry

• Unified Code for Units of Measure (UCUM)Unified Code for Units of Measure (UCUM)• comprehensive vocabulary of units of measures, comprehensive vocabulary of units of measures,

semantically enabledsemantically enabled• supporting seamless auto-conversion between supporting seamless auto-conversion between

unitsunits• realistic, practical, includes customary unitsrealistic, practical, includes customary units


What Others Say: CDCWhat Others Say: CDC

““HL7 is the undisputed leader in the establishment of standards for interoperability among computerized information systems in healthcare. A key aspect of the HL7 methodology is the HL7 Reference Information Model (HL7 RIM).”

US. Dept. For Health and Human Services, Public Health Service, Centers For Disease Control and Prevention. Public Health Conceptual Data Model. July 2000.


What Others Say: NCVHSWhat Others Say: NCVHS

““NCVHS recommends that HL7 be recognized NCVHS recommends that HL7 be recognized as the core PMRI standard.”as the core PMRI standard.”““NCVHS recommends that HHS provide NCVHS recommends that HHS provide incentives to accelerate the development incentives to accelerate the development and early adoption of HL7 version 3 and early adoption of HL7 version 3 standards.”standards.”““HHS should encourage PMRI SDOs to HHS should encourage PMRI SDOs to harmonize their data elements and data harmonize their data elements and data definitions for future versions so that they definitions for future versions so that they are consistent with the HL7 Reference are consistent with the HL7 Reference Information Model (RIM).”Information Model (RIM).”

Recommendation Letter from the National Council of Vital and Health Statistics to the Secretary U.S. Department of Health and Human Services.


What Others Say: AAMCWhat Others Say: AAMC

“An optimal clinical information system for patient care and clinical research [depends upon] common standards […]. Existing standards such as Health Level Seven (HL7) for message data interchange and Logical Observation Identifier Names and Codes (LOINC) […] have the potential to make data more consistent and comparable. […] Clinical research should not create new standards; rather, it should build its requirements into the standards now being developed, using the capabilities they provide.”

Information Technology Enabling Research: Information Technology Enabling Research: Findings and Recommendations from a Conference Sponsored by the Association of American Medical Colleges with Funding from the National Science Foundation; October 30-31, 2002


HL7 Reference Information Model HL7 Reference Information Model (UML)(UML)

Account

name : STbalanceAmt : MOcurrencyCode : CEinterestRateQuantity : RTO<MO,PQ>allowedBalanceQuantity : IVL<MO>

DeviceTask

parameterValue : LIST<ANY>

DiagnosticImage

subjectOrientationCode : CE

Diet

energyQuantity : PQcarbohydrateQuantity : PQ

FinancialContract

paymentTermsCode : CE

FinancialTransaction

amt : MOcreditExchangeRateQuantity : REALdebitExchangeRateQuantity : REAL

InvoiceElement

modifierCode : SET<CE>unitQuantity : RTO<PQ,PQ>unitPriceAmt : RTO<MO,PQ>netAmt : MOfactorNumber : REALpointsNumber : REAL

ManagedParticipation

id : SET<II>statusCode : SET<CS>

Observation

value : ANYinterpretationCode : SET<CE>methodCode : SET<CE>targetSiteCode : SET<CD>

PatientEncounter

preAdmitTestInd : BLadmissionReferralSourceCode : CElengthOfStayQuantity : PQdischargeDispositionCode : CEspecialCourtesiesCode : SET<CE>specialAccommodationCode : SET<CE>acuityLevelCode : CE

Procedure

methodCode : SET<CE>approachSiteCode : SET<CD>targetSiteCode : SET<CD>

PublicHealthCase

detectionMethodCode : CEtransmissionModeCode : CEdiseaseImportedCode : CE

SubstanceAdministration

routeCode : CEapproachSiteCode : SET<CD>doseQuantity : IVL<PQ>rateQuantity : IVL<PQ>doseCheckQuantity : SET<RTO>maxDoseQuantity : SET<RTO>

Supply

quantity : PQexpectedUseTime : IVL<TS>

WorkingList

ownershipLevelCode : CE

Container

capacityQuantity : PQheightQuantity : PQdiameterQuantity : PQcapTypeCode : CEseparatorTypeCode : CEbarrierDeltaQuantity : PQbottomDeltaQuantity : PQ

Device

manufacturerModelName : SCsoftwareName : SClocalRemoteControlStateCode : CE...alertLevelCode : CElastCalibrationTime : TS

LivingSubject

administrativeGenderCode : CEbirthTime : TSdeceasedInd : BLdeceasedTime : TSmultipleBirthInd : BLmultipleBirthOrderNumber : INTorganDonorInd : BL

ManufacturedMaterial

lotNumberText : STexpirationTime : IVL<TS>stabilityTime : IVL<TS>

Material

formCode : CENonPersonLivingSubject

strainText : EDgenderStatusCode : CE

Organization

addr : BAG<AD>standardIndustryClassCode : CE

Person

addr : BAG<AD>maritalStatusCode : CEeducationLevelCode : CEraceCode : SET<CE>disabilityCode : SET<CE>livingArrangementCode : CEreligiousAffiliationCode : CEethnicGroupCode : SET<CE>

Place

mobileInd : BLaddr : ADdirectionsText : EDpositionText : EDgpsText : ST

Access

approachSiteCode : CDtargetSiteCode : CDgaugeQuantity : PQ

Employee

jobCode : CEjobTitleName : SCjobClassCode : CEsalaryTypeCode : CEsalaryQuantity : MOhazardExposureText : EDprotectiveEquipmentText : ED

LicensedEntity

recertificationTime : TS

Patient

confidentialityCode : CEveryImportantPersonCode : CE

ActRelationship

typeCode : CSinversionInd : BLcontextControlCode : CScontextConductionInd : BLsequenceNumber : INTpriorityNumber : INTpauseQuantity : PQcheckpointCode : CSsplitCode : CSjoinCode : CSnegationInd : BLconjunctionCode : CSlocalVariableName : STseperatableInd : BL

Act

classCode : CSmoodCode : CSid : SET<II>code : CDnegationInd : BLderivationExpr : STtext : EDtitle : STstatusCode : SET<CS>effectiveTime : GTSactivityTime : GTSavailabilityTime : TSpriorityCode : SET<CE>confidentialityCode : SET<CE>...repeatNumber : IVL<INT>interruptibleInd : BLlevelCode : CEindependentInd : BLuncertaintyCode : CEreasonCode : SET<CE>languageCode : CE

0..n

1

outboundRelationship

0..n

source1

0..n

1

inboundRelationship 0..n

target

1

LanguageCommunication

languageCode : CEmodeCode : CEproficiencyLevelCode : CEpreferenceInd : BL

Participation

typeCode : CSfunctionCode : CDcontextControlCode : CS...sequenceNumber : INTnegationInd : BLnoteText : EDtime : IVL<TS>modeCode : CEawarenessCode : CEsignatureCode : CEsignatureText : EDperformInd : BLsubstitutionConditionCode : CE...

0..n

1

0..n

1

Entity

classCode : CSdeterminerCode : CSid : SET<II>code : CEquantity : SET<PQ>name : BAG<EN>desc : EDstatusCode : SET<CS>existenceTime : IVL<TS>...telecom : BAG<TEL>riskCode : CEhandlingCode : CE

1

0..n

1

0..n

RoleLink

typeCode : CSeffectiveTime : IVL<TS>...

Role

classCode : CSid : SET<II>code : CEnegationInd : BLaddr : BAG<AD>telecom : BAG<TEL>statusCode : SET<CS>effectiveTime : IVL<TS>certificateText : EDquantity : RTOpositionNumber : LIST<INT>...

0..n

1

0..n

10..n0..1

playedRole

0..n

player

0..1

0..n0..1

scopedRole

0..n

scoper

0..1

0..n

1

outboundLink 0..n

source

1

0..n

1

inboundLink

0..n

target1

RIM 2.01July 17,2003

ControlAct


HL7 RIM Backbone (UML)HL7 RIM Backbone (UML)ActRelationship

typeCode : CSinversionInd : BL

contextControlCode : CScontextConductionInd : BLsequenceNumber : INT

priorityNumber : INTpauseQuantity : PQcheckpointCode : CSsplitCode : CS

joinCode : CSnegationInd : BLconjunctionCode : CSlocalVariableName : STseperatableInd : BL

Act

classCode : CS

moodCode : CSid : SET<II>code : CDnegationInd : BLderivationExpr : STtext : EDtitle : STstatusCode : SET<CS>effectiveTime : GTSactivityTime : GTS

availabilityTime : TSpriorityCode : SET<CE>confidentialityCode : SET<CE>

repeatNumber : IVL<INT>interruptibleInd : BLlevelCode : CE

independentInd : BLuncertaintyCode : CEreasonCode : SET<CE>languageCode : CE

0..n

1

outboundRelationship

0..n

source1

0..n

1

inboundRelationship 0..n

target

1

Participation

typeCode : CSfunctionCode : CDcontextControlCode : CS...sequenceNumber : INTnegationInd : BLnoteText : EDtime : IVL<TS>modeCode : CEawarenessCode : CEsignatureCode : CE

signatureText : EDperformInd : BLsubstitutionConditionCode : CE...

0..n

1

0..n

1

Entity

classCode : CS

determinerCode : CSid : SET<II>code : CE

quantity : SET<PQ>name : BAG<EN>desc : EDstatusCode : SET<CS>

existenceTime : IVL<TS> ...telecom : BAG<TEL>riskCode : CE

handlingCode : CE

RoleLink

typeCode : CS

effectiveTime : IVL<TS>...

Role

classCode : CS

id : SET<II>code : CEnegationInd : BL

addr : BAG<AD>telecom : BAG<TEL>statusCode : SET<CS>

effectiveTime : IVL<TS>certificateText : EDquantity : RTOpositionNumber : LIST<INT>...

0..n

1

0..n

10..n0..1

playedRole

0..n

player

0..1

0..n0..1

scopedRole

0..n

scoper

0..1

0..n

1

outboundLink 0..n

source

1

0..n

1

inboundLink

0..n

target1


HL7 RIM Backbone as Block-DiagramHL7 RIM Backbone as Block-Diagram

EntityclassCode *: <= ENTdeterminerCode *: <= INSTANCEid: SET<II> [0..*]code: CE CWE [0..1] <= EntityCodequantity: SET<PQ> [0..*]name: BAG<EN> [0..*]desc: ED [0..1]statusCode: SET<CS> CNE [0..*] <= EntityStatusexistenceTime: IVL<TS> [0..1]telecom: BAG<TEL> [0..*]riskCode: CE CWE [0..1] <= EntityRiskhandlingCode: CE CWE [0..1] <= EntityHandling

Entity

ActclassCode *: <= ACTmoodCode *: <= EVNid: SET<II> [0..*]code: CD CWE [0..1] <= ActCodenegationInd: BL [0..1]derivationExpr: ST [0..1]text: ED [0..1]statusCode: SET<CS> CNE [0..*] <= ActStatuseffectiveTime: GTS [0..1]activityTime: GTS [0..1]availabilityTime: TS [0..1]priorityCode: SET<CE> CWE [0..*] <= ActPriorityconfidentialityCode: SET<CE> CWE [0..*] <= ConfidentialityrepeatNumber: IVL<INT> [0..1]interruptibleInd: BL [0..1]levelCode: CE CWE [0..1] <= ActContextLevelindependentInd: BL [0..1]uncertaintyCode: CE CNE [0..1] <= ActUncertaintyreasonCode: SET<CE> CWE [0..*] <= ActReasonlanguageCode: CE CWE [0..1] <= HumanLanguage

0..* source

0..* target

typeCode *: <= ActRelationshipTypeinversionInd: BL [0..1]contextControlCode: CS CNE [0..1] <= ContextControlcontextConductionInd: BL [0..1]sequenceNumber: INT [0..1]priorityNumber: INT [0..1]pauseQuantity: PQ [0..1]checkpointCode: CS CNE [0..1] <= ActRelationshipCheckpointsplitCode: CS CNE [0..1] <= ActRelationshipSplitjoinCode: CS CNE [0..1] <= ActRelationshipJoinnegationInd: BL [0..1]conjunctionCode: CS CNE [0..1] <= RelationshipConjunctionlocalVariableName: ST [0..1]seperatableInd: BL [0..1]

sourceOf /targetOf

Act

0..1 playingEntity

0..1 scopingEntity

Role 0..* scopedRole

0..* playedRole

classCode *: <= ROLid: SET<II> [0..*]code: CE CWE [0..1] <= RoleCodenegationInd: BL [0..1]addr: BAG<AD> [0..*]telecom: BAG<TEL> [0..*]statusCode: SET<CS> CNE [0..*] <= RoleStatuseffectiveTime: IVL<TS> [0..1]certificateText: ED [0..1]quantity: RTO<QTY,QTY> [0..1]positionNumber: LIST<INT> [0..*]

0..* act

0..* participant

typeCode *: <= ParticipationTypefunctionCode: CD CWE [0..1] <= ParticipationFunctioncontextControlCode: CS CNE [0..1] <= ContextControlsequenceNumber: INT [0..1]negationInd: BL [0..1]noteText: ED [0..1]time: IVL<TS> [0..1]modeCode: CE CWE [0..1] <= ParticipationModeawarenessCode: CE CWE [0..1] <= TargetAwarenesssignatureCode: CE CNE [0..1] <= ParticipationSignaturesignatureText: ED [0..1]performInd: BL [0..1]

participant / participation


HL7 Data in XMLHL7 Data in XML<act classCode=“ACT” moodCode=“…”><act classCode=“ACT” moodCode=“…”>

<id root=“1.3.6.1.4.1.12009.3” extension=“A1234”/><id root=“1.3.6.1.4.1.12009.3” extension=“A1234”/><code code=“...” codeSystem=“2.16.840.1.113883.6.1”/><code code=“...” codeSystem=“2.16.840.1.113883.6.1”/><participant typeCode=“…”><participant typeCode=“…”>

<participant classCode=“ROL”><participant classCode=“ROL”><id root=“1.3.6.1.4.1.12009.4” extension=“1234567-8”/><id root=“1.3.6.1.4.1.12009.4” extension=“1234567-8”/><code code=“…” codeSystem=“2.16.840.1.113883.6.21”/><code code=“…” codeSystem=“2.16.840.1.113883.6.21”/><playingEntity classCode=“ENT”><playingEntity classCode=“ENT”>

<name>...</name><name>...</name></playingEntity></playingEntity><scopingEntity classCode=“ENT”><scopingEntity classCode=“ENT”>

<name>...</name><name>...</name></scopingEntity></scopingEntity>

</participant></participant></participant></participant><sourceOf typeCode=“REL”><sourceOf typeCode=“REL”>

<target classCode=“ACT”><target classCode=“ACT”><id root=“1.3.6.1.4.1.12009.3” extension=“A1235”/><id root=“1.3.6.1.4.1.12009.3” extension=“A1235”/>

</target></target></sourceOf></sourceOf>

</act></act>


Refined Model – Observation on PatientRefined Model – Observation on Patient

PersonclassCode *: <= PSNdeterminerCode *: <= INSTANCEid: SET<II> [0..*]code: CE CWE [0..1] <= EntityCodename: BAG<EN> [0..*]riskCode: CE CWE [0..1] <= EntityRiskhandlingCode: CE CWE [0..1] <= EntityHandlingadministrativeGenderCode: CE CWE [0..1] <= AdministrativeGenderbirthTime: TS [0..1]deceasedTime: TS [0..1]maritalStatusCode: CE CWE [0..1] <= MaritalStatuseducationLevelCode: CE CWE [0..1] <= EducationLeveldisabilityCode: SET<CE> CWE [0..*] <= PersonDisabilityTypelivingArrangementCode: CE CWE [0..1] <= LivingArrangementreligiousAffiliationCode: CE CWE [0..1] <= ReligiousAffiliationraceCode: SET<CE> CWE [0..*] <= RaceethnicGroupCode: SET<CE> CWE [0..*] <= Ethnicity

OrganizationclassCode *: <= ORGdeterminerCode *: <= INSTANCEname: BAG<EN> [0..*]standardIndustryClassCode: CE CWE [0..1] <= OrganizationIndustryClass

ObservationEventclassCode *: <= OBSmoodCode *: <= EVNid*: II [1..1]code*: CD CWE [1..1] <= ObservationTypetext: ED [0..1]statusCode*: CS CNE [1..1] <= completedeffectiveTime*: IVL<TS> [1..1]confidentialityCode: SET<CE> CWE [0..*] <= Confidentiality

0..* observationEventtypeCode *: <= COMP

component

ObservationEventclassCode *: <= OBSmoodCode *: <= EVNid*: II [1..1]code*: CD CWE [1..1] <= ObservationTypestatusCode: CS CNE [1..1] <= completedeffectiveTime*: IVL<TS> [0..1]confidentialityCode: SET<CE> CWE [0..*] <= Confidentiality

0..1 patientPerson

0..1 providerOrganization

Patient 0..* patient

0..* healthCareProvider

classCode *: <= PATid: SET<II> [0..*]code: CE CWE [0..1] <= RoleCodeaddr: BAG<AD> [0..*]telecom: BAG<TEL> [0..*]statusCode: SET<CS> CNE [0..*] <= RoleStatuseffectiveTime: IVL<TS> [0..1]confidentialityCode: CE CWE [0..1] <= ConfidentialityveryImportantPersonCode: CE CWE [0..1] <= PatientImportance

0..* patient

typeCode *: <= SBJawarenessCode: CE CWE [0..1] <= TargetAwareness

subject


Observation on Patient in XMLObservation on Patient in XML<observationEvent classCode=“OBS” moodCode=“EVN”><observationEvent classCode=“OBS” moodCode=“EVN”>

<id root=“1.3.6.1.4.1.12009.3” extension=“A1234”/><id root=“1.3.6.1.4.1.12009.3” extension=“A1234”/><code code=“...” codeSystem=“2.16.840.1.113883.6.1”/><code code=“...” codeSystem=“2.16.840.1.113883.6.1”/><subject typeCode=“…”><subject typeCode=“…”>

<patient classCode=“ROL”><patient classCode=“ROL”><id root=“1.3.6.1.4.1.12009.4” extension=“1234567-8”/><id root=“1.3.6.1.4.1.12009.4” extension=“1234567-8”/><code code=“…” codeSystem=“2.16.840.1.113883.6.21”/><code code=“…” codeSystem=“2.16.840.1.113883.6.21”/><patientPerson classCode=“PSN”><patientPerson classCode=“PSN”>

<name><given>John</given><family>Doe</family></name><name><given>John</given><family>Doe</family></name></patientPerson></patientPerson><providerOrganization classCode=“ORG”><providerOrganization classCode=“ORG”>

<name>St., Josephs Hospital</name><name>St., Josephs Hospital</name></providerOrganization></providerOrganization>

</patient></patient></subject></subject><component typeCode=“REL”><component typeCode=“REL”>

<observationEvent classCode=“ACT”><observationEvent classCode=“ACT”><id root=“1.3.6.1.4.1.12009.3” extension=“A1235”/><id root=“1.3.6.1.4.1.12009.3” extension=“A1235”/>

</observationEvent></observationEvent></component></component>

</observationEvent></observationEvent>


Refined Model – Observation on Trial Refined Model – Observation on Trial SubjectSubject

PersonclassCode *: <= PSNdeterminerCode *: <= INSTANCEid: SET<II> [0..*]code: CE CWE [0..1] <= EntityCodename: BAG<EN> [0..*]riskCode: CE CWE [0..1] <= EntityRiskhandlingCode: CE CWE [0..1] <= EntityHandlingadministrativeGenderCode: CE CWE [0..1] <= AdministrativeGenderbirthTime: TS [0..1]deceasedTime: TS [0..1]maritalStatusCode: CE CWE [0..1] <= MaritalStatuseducationLevelCode: CE CWE [0..1] <= EducationLeveldisabilityCode: SET<CE> CWE [0..*] <= PersonDisabilityTypelivingArrangementCode: CE CWE [0..1] <= LivingArrangementreligiousAffiliationCode: CE CWE [0..1] <= ReligiousAffiliationraceCode: SET<CE> CWE [0..*] <= RaceethnicGroupCode: SET<CE> CWE [0..*] <= Ethnicity

OrganizationclassCode *: <= ORGdeterminerCode *: <= INSTANCEname: BAG<EN> [0..*]standardIndustryClassCode: CE CWE [0..1] <= OrganizationIndustryClass

ObservationEventclassCode *: <= OBSmoodCode *: <= EVNid*: II [1..1]code*: CD CWE [1..1] <= ObservationTypetext: ED [0..1]statusCode*: CS CNE [1..1] <= completedeffectiveTime*: IVL<TS> [1..1]confidentialityCode: SET<CE> CWE [0..*] <= Confidentiality

0..* observationEventtypeCode *: <= COMP

component

ObservationEventclassCode *: <= OBSmoodCode *: <= EVNid*: II [1..1]code*: CD CWE [1..1] <= ObservationTypestatusCode: CS CNE [1..1] <= completedeffectiveTime*: IVL<TS> [0..1]confidentialityCode: SET<CE> CWE [0..*] <= Confidentiality

0..1 subjectPerson

0..1 researchSponsor

ResearchSubject 0..* sponsoredSubject

0..* subjectOf

classCode *: <= RESBJid: SET<II> [0..*]code: CE CWE [0..1] <= RoleCodeaddr: BAG<AD> [0..*]telecom: BAG<TEL> [0..*]statusCode: SET<CS> CNE [0..*] <= RoleStatuseffectiveTime: IVL<TS> [0..1]

0..* researchSubject

typeCode *: <= SBJ

subject


Observation on Trial Subject in XMLObservation on Trial Subject in XML<observationEvent classCode=“OBS” moodCode=“EVN”><observationEvent classCode=“OBS” moodCode=“EVN”>

<id root=“1.3.6.1.4.1.12009.3” extension=“A1234”/><id root=“1.3.6.1.4.1.12009.3” extension=“A1234”/><code code=“...” codeSystem=“2.16.840.1.113883.6.1”/><code code=“...” codeSystem=“2.16.840.1.113883.6.1”/><subject typeCode=“…”><subject typeCode=“…”>

<researchSubject classCode=“ROL”><researchSubject classCode=“ROL”><id root=“1.3.6.1.4.1.12009.5” extension=“1234567-8”/><id root=“1.3.6.1.4.1.12009.5” extension=“1234567-8”/><code code=“…” codeSystem=“2.16.840.1.113883.6.21”/><code code=“…” codeSystem=“2.16.840.1.113883.6.21”/><subjectPerson classCode=“PSN”><subjectPerson classCode=“PSN”>

<name><given>John</given><family>Doe</family></name><name><given>John</given><family>Doe</family></name></subjectPerson></subjectPerson><researchSponsor classCode=“ORG”><researchSponsor classCode=“ORG”>

<name>Eli Lilly</name><name>Eli Lilly</name></researchSponsor></researchSponsor>

</researchSubject></researchSubject></subject></subject><component typeCode=“REL”><component typeCode=“REL”>

<observationEvent classCode=“ACT”><observationEvent classCode=“ACT”><id root=“1.3.6.1.4.1.12009.3” extension=“A1235”/><id root=“1.3.6.1.4.1.12009.3” extension=“A1235”/>

</observationEvent></observationEvent></component></component>

</observationEvent></observationEvent>


Data Types for Biomedical Data Types for Biomedical InformationInformation

• Medical information needs more than just Medical information needs more than just string, int and float.string, int and float.

• Coded data: code, codeSystem, Coded data: code, codeSystem, displayName, originalText.displayName, originalText.

• Measurement values (physical quantities) Measurement values (physical quantities) value and unit.value and unit.

• Incomplete information (null flavors): not Incomplete information (null flavors): not applicable, unknown, vs. not asked.applicable, unknown, vs. not asked.

• Uncertain values with probabilities and Uncertain values with probabilities and distributions, aggregate distribution data.distributions, aggregate distribution data.

• Correlated data series, time series, Correlated data series, time series, multidimensional data.multidimensional data.


Current Applications of HL7 v3Current Applications of HL7 v3

• Traditional individual health careTraditional individual health care• New Frontiers:New Frontiers:

• Laboratory AutomationLaboratory Automation• Veterinary medicine (AVMA)Veterinary medicine (AVMA)• Public health (CDC’s PHDM)Public health (CDC’s PHDM)• Food and Drug Safety (FDA)Food and Drug Safety (FDA)

• Clinical Trials Reporting (FDA, CDISC)Clinical Trials Reporting (FDA, CDISC)• Chemical Stability Testing (FDA)Chemical Stability Testing (FDA)• Adverse Event Reporting (FDA, E2BM)Adverse Event Reporting (FDA, E2BM)

• Clinical GenomicsClinical Genomics• Implantable Devices – CardiologyImplantable Devices – Cardiology• Patient SafetyPatient Safety


Advantages of HL7 and the RIMAdvantages of HL7 and the RIM

• make data more consistent and make data more consistent and comparablecomparable

• reduce differences at overlaps reduce differences at overlaps between specialty standardsbetween specialty standards

• common data-patterns for common common data-patterns for common problemsproblems

• highly flexible and deep model of highly flexible and deep model of medical information medical information

• minimize cost of data collection by minimize cost of data collection by tapping into existing data streamstapping into existing data streams


HL7 for Biomedical ResearchHL7 for Biomedical Research

• Regulated Clinical Research Regulated Clinical Research Information Management Information Management Technical Committee (RCRIM)Technical Committee (RCRIM)

• Clinical Genomics Special Clinical Genomics Special Interest Group (CG SIG)Interest Group (CG SIG)

• Orders and Observations Orders and Observations Technical CommitteeTechnical Committee


R Clinical Research IM TCR Clinical Research IM TC

• Clinical trials related medical Clinical trials related medical informationinformation

• Clinical trials protocols Clinical trials protocols specification frameworkspecification framework

• Surveillance, product labeling, Surveillance, product labeling, regulatory documentsregulatory documents

• Collaborative with industry and Collaborative with industry and government (e.g., Lilly, FDA, government (e.g., Lilly, FDA, CDISC)CDISC)


Clinical Genomics SIGClinical Genomics SIG

• support application of genomics support application of genomics in clinical medicinein clinical medicine

• specify use-cases and data specify use-cases and data requirementsrequirements

• review existing genomics review existing genomics specificationsspecifications

• recommend enhancements to recommend enhancements to HL7 standards to support HL7 standards to support genomicsgenomics


0..1 individualAllele

typeCode*: <= COMP

component3

0..* priorClinicalPhenotype

typeCode*: <= SEQL

sequelTo

IndividualAlleleclassCode *: <= OBSmoodCode *: <= EVNcode*: CE CWE [1..1] (allele identifier & classification, e.g. GeneBank)text: ED

SNPclassCode *: <= OBSmoodCode *: <= EVNid: II [0..1]code: CE CWE (SNP identifier & classification, e.g.Entrez dbSNP)text: EDvalue: ANY [0..1] (the SNP itself)methodCode: SET<CE> CWE

SNP_HaplotypeclassCode *: <= OBSmoodCode *: <= EVNid: II [0..1]code: CE CWE

GenotypeclassCode *: <= OBSmoodCode *: <= EVNid: II [0..1]code: CE CWE (e.g., HETEROZYGOTE)text: ED

0..* haplotype

typeCode*: <= COMP

componentOf

1..1 individualAllele

typeCode *: <= COMP

component2

0..* pertinentSNP

typeCode*: <= PERT

pertinentInformation1

AlleleSequenceclassCode *: <= OBSmoodCode *: <= EVNid: II [0..1]code: [1..1] (the sequence standard code, e.g.BSML, GMS)text: (the annotated sequence)effectiveTime: [1..1]value: ED [1..1] (the actual sequence)methodCode: (the sequencingmethod)

0..1 pertinentAlleleSequence

typeCode*: <= PERT


GeneExpressionclassCode *: <= OBSmoodCode *: <= EVNid: II [0..1]code: CE CWE [0..1] <= ActCode (the standard's code (e.g., MAGE-ML identifier)text: ED [0..1]effectiveTime: GTS [0..1]value: ED [1..1] (the actual gene expression levels)methodCode: SET<CE> CWE [0..*]

0..1 pertinentGeneExpression

typeCode *: <= PERT


HaplotypeclassCode *: <= ACTmoodCode *: <= EVNid: II [0..1]code: CE CWE (haplotype identifier and classification, e.g.,Entrez)

PolypeptideclassCode *: <= OBSmoodCode *: <= EVNid: II [0..1]code*: CE CWE [1..1](idnetifier & classification ofthe protein, e.g., SwissProt,) (PDB, PIR, HUPO)text:

0..* outcomePolypeptide

typeCode*: <= OUTC

outcome

DeterminantPeptideclassCode *: <= OBSmoodCode *: <= EVNid: II [0..1]code: CE CWE (identifier and classification of the determinant, e.g., Entrez)text: ED

0..* pertinentDeterminantPeptide

typeCode *: <= PERT


MutationclassCode *: <= OBSmoodCode *: <= EVNid: II [0..1]code: CE CWE (mutation identifier andclassification, e.g. LOINC MOLECULARGENETICS NAMING)text:

0..* pertinentMutation

typeCode *: <= PERT


ClinicalPhenotypeclassCode *: <= OBSmoodCode *: <= EVNid: II [0..1]code: CE CWE [0..1] (disease, allergy, sensitivity, ADE, etc.)text: ED [0..1]uncertaintyCode: CE CNE [0..1]value: ANY [0..1]

Genotype

SNP_Haplotype


typeCode*: <= SEQL

sequelTo

HL7 Clinical Genomics SIGDocument: Individual Genotype DIM (to be used as a CMET or similar mechanism)Subject: Genomics Data Rev: 0.4 Date: September 12, 2003Authors: Amnon Shabo (IBM Research in Haifa), Shosh Israel (Hadassah University Hospital)

CGSIG(CGEN_RM000002)

Clinical-GenomicsEntry point to theGenotype Model

IndividualAllele0..1 individualAllele

typeCode*: <= COMP

component1

Note:This IndividualAllele is a shadow andtogether with the main one, both allelesrepresent the allele pair on the paternaland maternal chromosomes.

Mutation

0..1 pertinentMutation

typeCode*: <= PERT

pertinentInformation

0..* sNP_Haplotype

typeCode*: <= COMP

componentOf

Constrained to a restricted MAGE-MLcontent model, specified elesewhere.

Constraint: GeneExpression.value

Constrained to a restrictedBSML or GMS content model,specified elsewhere.

Constraint: AlleleSequence.value

MethodclassCode *: <= PROCmoodCode *: <= EVNid: II [0..1]code: CD CWE [0..1] <=ActCode (type of method)text: ED [0..1] (free text description of themethod used)methodCode: SET<CE> CWE[0..*]


typeCode*: <= SEQL

sequelTo

IndividualAllele

Note:The third allele is optionaland could be present if thepatient has three copies ofa chromosome as in theDown’s Syndrome.

0..* pertinentIndividualAllele

typeCode *: <= PERT


Note:A related allele that is on adifferent haplotype, and stillhas significant interrelationwith the source allele.(could be attached to itselfrecursively)

IndividualAllele


typeCode*: <= SEQL

sequelTo

ExternalClinicalPhenotypeclassCode *: <= OBSmoodCode *: <= EVNid*: II [1..1] (The id of an external observation (e.g., in a problemlist)

Note:An external observation is a valid Observationinstance existing in any other HL7-compliantartifact, e.g., a document or a message.

Note:An observation of a clinical conditionrepresented internally in this model.

Note: Shadowed observationsare copies of otherobservations and thus have allof the original act attributes.

DeterminantPeptide

Note:Use methodCode ifyou don’t use theassociated methodprocedure.

Note:Could refine ActRelationship typeCodeto elaborate on different types of genomicto phenotype effects.

Method0..* pertinentMethod

typeCode*: <= PERT

pertinentInformation

Note:Usually this is a computed outcome, i.e.,the lab does not produce the actualprotein.

0..* referredToExternalClinicalPhenotype

typeCode*: <= x_ActRelationshipExternalReference

reference

0..* pertinentMethod

typeCode*: <= PERT



HL7 CT SIG and other HL7 CT SIG and other Specifications in BioinformaticsSpecifications in Bioinformatics

• CT SIG understands that there exist other CT SIG understands that there exist other specifications in the field:specifications in the field:• Bioinformatic Sequence Markup Language (BSML)Bioinformatic Sequence Markup Language (BSML)• Microarray Gene Expression Markup Language Microarray Gene Expression Markup Language

(MAGE-ML)(MAGE-ML)• Interoperable Informatics Infrastructure Interoperable Informatics Infrastructure

Consortium (I3C)Consortium (I3C)• Systems Biology Markup Language (SBML)Systems Biology Markup Language (SBML)• CellML, BioML, MoDL …CellML, BioML, MoDL …

• There is significant overlap between those, There is significant overlap between those, which one should one pick?which one should one pick?

• It’s easy to make an XML schema for a It’s easy to make an XML schema for a special purpose, but how does it integrate?special purpose, but how does it integrate?


Myths and Facts about HL7Myths and Facts about HL7

• HL7 is only about EDI HL7 is only about EDI messaging in messaging in hospitalshospitals

• Must pay royalties to Must pay royalties to use the HL7 use the HL7 specificationsspecifications

• Must be a member to Must be a member to use the HL7 use the HL7 specificationsspecifications

• Must be a member to Must be a member to participate in participate in developmentdevelopment

• HL7 develops HL7 develops information modelsinformation models

• Final specification Final specification must be purchased, must be purchased, no fee for useno fee for use

• No fee for useNo fee for use• HL7 invites all HL7 invites all

stakeholders to stakeholders to participateparticipate

• Members can vote, Members can vote, membership open to membership open to anyoneanyone


Take-Home PointsTake-Home Points

• Data integration problem is not Data integration problem is not technological but conceptualtechnological but conceptual

• Making a special XML schema is easyMaking a special XML schema is easy• With HL7 you think integrated across With HL7 you think integrated across

specialty applicationsspecialty applications• Unlikely that clinical research needs Unlikely that clinical research needs

require special technologyrequire special technology• The general model facilitates The general model facilitates

harmonization and interoperabilityharmonization and interoperability• HL7 has what it takes, work with itHL7 has what it takes, work with it


thank youthank you

Gunther Schadow,Gunther Schadow,Regenstrief Institute, Inc.Regenstrief Institute, Inc.1050 Wishard Blvd.1050 Wishard Blvd.Indianapolis, IN 46202Indianapolis, IN [email protected]@regenstrief.org

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