Transcript HL7 The Data Standard for Biomedical Informatics

HL7 The Data Standard for
Biomedical Informatics
GCRC Biomedical Informatics Workshop
October 29-30, 2003, Bethesda, MD
Gunther Schadow, MD, PhD
Regenstrief Institute, Indiana
University School of Medicine,
Indianapolis, IN
What is HL7?
• ANSI accredited Standard Development
Organization (SDO) to provide standards for
• the exchange, management and integration of
• data that support
• clinical patient care and the
• management, delivery and evaluation of
healthcare services. Specifically, to
• create flexible, cost effective
• approaches, standards, guidelines,
methodologies, and related services for
• interoperability between healthcare
information systems.
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What HL7 Products Exist?
• HL7 version 2 messaging standards for
• Patient administration, Order Entry, Results
• Medical data “attachments” to HIPAA
transactions
• HL7 version 3 specifications for
•
•
•
•
•
•
all of the above, plus
Clinical Document Architecture
Reference Information Model (RIM) for Healthcare
includes Data Type Specification for health care
XML Data Formats for Medical Information
Controlled Vocabulary
• Others (by acquisition)
• Arden Syntax
• C-COW (clinical desktop integration)
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Good friends of HL7
• Logical Observation Identifiers, Names and
Codes (LOINC)
• vocabulary of medical observations (laboratory
and clinical)
• practical developed for and with the industry
• Unified Code for Units of Measure (UCUM)
• comprehensive vocabulary of units of measures,
semantically enabled
• supporting seamless auto-conversion between
units
• realistic, practical, includes customary units
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What 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.
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What Others Say: NCVHS
“NCVHS recommends that HL7 be recognized
as the core PMRI standard.”
“NCVHS recommends that HHS provide
incentives to accelerate the development and
early adoption of HL7 version 3 standards.”
“HHS should encourage PMRI SDOs to
harmonize their data elements and data
definitions for future versions so that they are
consistent with the HL7 Reference 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.
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What 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: 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
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HL7 Reference Information Model (UML)
Place
Patient
mobileInd : BL
addr : AD
directionsText : ED
positionText : ED
gpsText : ST
confidentialityCode : CE
veryImportantPersonCode : CE
Organization
addr : BAG<AD>
standardIndustryClassCode : CE
ActRelationship
ManagedParticipation
typeCode : CS
id : SET<II>
inversionInd : BL
outboundRelationship
statusCode : SET<CS>
contextControlCode : CS
Access
LicensedEntity
0..n contextConductionInd : BL
approachSiteCode : CD
sequenceNumber : INT
recertificationTime : TS
Person
targetSiteCode : CD
1 source
priorityNumber : INT
gaugeQuantity : PQ
addr : BAG<AD>
pauseQuantity : PQ
Act
Participation
maritalStatusCode : CE
checkpointCode : CS
classCode
:
CS
educationLevelCode : CE
Entity
typeCode : CS
splitCode : CS
Role
moodCode
:
CS
raceCode : SET<CE>
classCode : CS
functionCode : CD
player
joinCode : CS
id
:
SET<II>
disabilityCode : SET<CE>
classCode : CS
contextControlCode : CS
...
determinerCode : CS
negationInd : BL
0..1
code : CD
0..n
livingArrangementCode : CE
id
:
SET<II>
sequenceNumber
:
INT
id : SET<II>
0..n
conjunctionCode : CS
1
negationInd
:
BL
religiousAffiliationCode : CE
code
:
CE
code : CE
playedRole
negationInd : BL
localVariableName : ST
1
derivationExpr
:
ST
ethnicGroupCode : SET<CE>
negationInd : BL
quantity : SET<PQ>
0..n noteText : ED
seperatableInd : BL
text
:
ED
addr : BAG<AD>
time : IVL<TS>
name : BAG<EN>
inboundRelationship 0..n
title
:
ST
telecom : BAG<TEL>
desc : ED
modeCode : CE
statusCode : SET<CS>
statusCode : SET<CS>
statusCode : SET<CS>
awarenessCode : CE
target
scopedRole
LivingSubject
effectiveTime : GTS
effectiveTime : IVL<TS>
signatureCode : CE
existenceTime : IVL<TS>...
0..n certificateText : ED
activityTime : GTS
1
administrativeGenderCode : CE
telecom : BAG<TEL>
signatureText : ED
0..1
availabilityTime : TS
birthTime : TS
quantity : RTO
source performInd : BL
riskCode : CE
ControlAct
deceasedInd : BL
scoper
positionNumber : LIST<INT>
... 1
substitutionConditionCode
... : CE priorityCode : SET<CE>
handlingCode : CE
confidentialityCode : SET<CE>...
deceasedTime : TS
1 target
repeatNumber : IVL<INT>
multipleBirthInd : BL
1
interruptibleInd : BL
multipleBirthOrderNumber : INT
WorkingList
levelCode : CE
organDonorInd : BL
Employee
outboundLink 0..n
FinancialContract
ownershipLevelCode : CE
independentInd : BL
0..n
jobCode : CE
RoleLink
paymentTermsCode : CE
uncertaintyCode : CE
jobTitleName : SC
Material
inboundLink typeCode : CS
reasonCode : SET<CE>
NonPersonLivingSubject
jobClassCode : CE
effectiveTime : IVL<TS>
...
formCode : CE
languageCode : CE
strainText : ED
salaryTypeCode : CE
salaryQuantity : MO
hazardExposureText : ED
protectiveEquipmentText : ED
genderStatusCode : CE
ManufacturedMaterial
lotNumberText : ST
expirationTime : IVL<TS>
stabilityTime : IVL<TS>
Device
0..n
LanguageCommunication
languageCode : CE
modeCode : CE
proficiencyLevelCode : CE
preferenceInd : BL
manufacturerModelName : SC
softwareName : SC
Container
localRemoteControlStateCode...: CE
capacityQuantity : PQ
alertLevelCode : CE
heightQuantity : PQ
lastCalibrationTime : TS
diameterQuantity : PQ
capTypeCode : CE
RIM 2.01
separatorTypeCode : CE
barrierDeltaQuantity : PQ
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bottomDeltaQuantity : PQ
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InvoiceElement
SubstanceAdministration
routeCode : CE
approachSiteCode : SET<CD>
doseQuantity : IVL<PQ>
rateQuantity : IVL<PQ>
doseCheckQuantity : SET<RTO>
maxDoseQuantity : SET<RTO>
Observation
value : ANY
interpretationCode : SET<CE>
methodCode : SET<CE>
targetSiteCode : SET<CD>
Procedure
methodCode : SET<CE>
approachSiteCode : SET<CD>
targetSiteCode : SET<CD>
DiagnosticImage
modifierCode : SET<CE>
unitQuantity : RTO<PQ,PQ>
unitPriceAmt : RTO<MO,PQ>
netAmt : MO
factorNumber : REAL
pointsNumber : REAL
Account
subjectOrientationCode : CE
PatientEncounter
PublicHealthCase
Supply
preAdmitTestInd : BL
admissionReferralSourceCode : CE
lengthOfStayQuantity : PQ
dischargeDispositionCode : CE
specialCourtesiesCode : SET<CE>
specialAccommodationCode : SET<CE>
acuityLevelCode : CE
detectionMethodCode : CE
transmissionModeCode : CE
diseaseImportedCode : CE
quantity : PQ
expectedUseTime : IVL<TS>
name : ST
balanceAmt : MO
currencyCode : CE
interestRateQuantity : RTO<MO,PQ>
allowedBalanceQuantity : IVL<MO>
FinancialTransaction
Diet
energyQuantity : PQ
carbohydrateQuantity : PQ
DeviceTask
parameterValue : LIST<ANY>
Copyright (c) 1999-2002 Regenstrief Institute for Health Care
amt : MO
creditExchangeRateQuantity : REAL
debitExchangeRateQuantity : REAL
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HL7 RIM Backbone (UML)
ActRelationship
Entity
classCode : CS
determinerCode : CS
id : SET<II>
code : CE
quantity : SET<PQ>
name : BAG<EN>
desc : ED
statusCode : SET<CS>
existenceTime : IVL<TS> ...
telecom : BAG<TEL>
riskCode : CE
handlingCode : CE
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player
0..1
0..n
playedRole
scopedRole
0..n
0..1
scoper
typeCode : CS
inversionInd : BL
outboundRelationship
contextControlCode : CS
0..n contextConductionInd : BL
sequenceNumber : INT
1 source
priorityNumber : INT
pauseQuantity : PQ
Act
Participation
checkpointCode : CS
classCode : CS
typeCode : CS
splitCode : CS
Role
moodCode : CS
functionCode : CD
joinCode : CS
id : SET<II>
classCode : CS
contextControlCode : CS...
negationInd : BL
code : CD
id : SET<II>
sequenceNumber : INT
0..n
conjunctionCode : CS
1
negationInd
:
BL
code : CE
negationInd : BL
localVariableName : ST
1 derivationExpr : ST
negationInd : BL
0..n noteText : ED
seperatableInd : BL
text
:
ED
addr : BAG<AD>
time : IVL<TS>
inboundRelationship 0..n
title : ST
telecom : BAG<TEL>
modeCode : CE
statusCode
:
SET<CS>
statusCode : SET<CS>
awarenessCode : CE
target
effectiveTime : GTS
effectiveTime : IVL<TS>
signatureCode : CE
activityTime : GTS
1
certificateText : ED
signatureText : ED
availabilityTime : TS
quantity : RTO
source performInd : BL
priorityCode : SET<CE>
positionNumber : LIST<INT>... 1
substitutionConditionCode
... : CE
confidentialityCode : SET<CE>
1 target
repeatNumber : IVL<INT>
interruptibleInd : BL
levelCode : CE
outboundLink 0..n
independentInd : BL
0..n
RoleLink
uncertaintyCode : CE
inboundLink typeCode : CS
reasonCode : SET<CE>
effectiveTime : IVL<TS>
...
languageCode : CE
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HL7 RIM Backbone as Block-Diagram
Entity
Act
classCode *: <= ACT
m oodCode *: <= EVN
0..* participant
id: SET<II> [0..*]
0..*participant
scopedRole / participation
code: CD CWE [0..1] <= ActCode
Role
type Code *: <= ParticipationType
negationInd: BL [0..1]
classCode *: <= ROL
functionCode: CD CWE [0..1] <= ParticipationFunction
derivationExpr: ST [0..1]
id: SET<II> [0..*]
contextControlCode: CS CNE [0..1] <= ContextControl
text: ED [0..1]
code: CE CWE [0..1] <= RoleCode
sequenceNumber: INT [0..1]
statusCode: SET<CS> CNE [0..*] <= ActStatus
negationInd: BL [0..1]
negationInd: BL [0..1]
effectiveTime: GTS [0..1]
addr: BAG<AD> [0..*]
noteText: ED [0..1]
activityTime: GTS [0..1]
telecom: BAG<TEL> [0..*]
time: IVL<TS> [0..1]
availabilityTime: TS [0..1]
statusCode: SET<CS> CNE [0..*] <= RoleStatus
modeCode: CE CWE [0..1] <= ParticipationMode
priorityCode: SET<CE> CWE [0..*] <= ActPriority
effectiveTime: IVL<TS> [0..1]
awarenessCode:
CE
CWE
[0..1]
<=
TargetAwareness
confidentialityCode: SET<CE> CWE [0..*] <= Confidentiality
certificateText: ED [0..1]
signatureCode:
CE
CNE
[0..1]
<=
ParticipationSignature
repeatNumber: IVL<INT> [0..1]
quantity: RTO<QTY,QTY> [0..1]
signatureText: ED [0..1]
interruptibleInd: BL [0..1]
positionNumber: LIST<INT> [0..*]
0..* playedRole
performInd: BL [0..1]
levelCode: CE CWE [0..1] <= ActContextLevel
0..* act independentInd: BL [0..1]
0..1 playingEntity
uncertaintyCode: CE CNE [0..1] <= ActUncertainty
Entity
reasonCode: SET<CE> CWE [0..*] <= ActReason
languageCode: CE CWE [0..1] <= HumanLanguage
classCode *: <= ENT
de te r m ine r Code *: <= INSTANCE
sourceOf /
id: SET<II> [0..*]
targetOf
code: CE CWE [0..1] <= EntityCode
type Code *: <= ActRelationshipType
quantity: SET<PQ> [0..*]
inversionInd: BL [0..1]
name: BAG<EN> [0..*]
contextControlCode: CS CNE [0..1] <= ContextControl
desc: ED [0..1]
contextConductionInd: BL [0..1]
statusCode: SET<CS> CNE [0..*] <= EntityStatus
sequenceNumber: INT [0..1]
existenceTime: IVL<TS> [0..1]
priorityNumber: INT [0..1]
telecom: BAG<TEL> [0..*]
pauseQuantity: PQ [0..1]
riskCode: CE CWE [0..1] <= EntityRisk
checkpointCode: CS CNE [0..1] <= ActRelationshipCheckpoint
handlingCode: CE CWE [0..1] <= EntityHandling
splitCode: CS CNE [0..1] <= ActRelationshipSplit
joinCode: CS CNE [0..1] <= ActRelationshipJoin
negationInd: BL [0..1]
conjunctionCode: CS CNE [0..1] <= RelationshipConjunction
localVariableName: ST [0..1]
seperatableInd: BL [0..1]
0..1 scopingEntity
0..* source
0..* target
Act
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HL7 Data in XML
<act classCode=“ACT” moodCode=“…”>
<id root=“1.3.6.1.4.1.12009.3” extension=“A1234”/>
<code code=“...” codeSystem=“2.16.840.1.113883.6.1”/>
<participant typeCode=“…”>
<participant classCode=“ROL”>
<id root=“1.3.6.1.4.1.12009.4” extension=“1234567-8”/>
<code code=“…” codeSystem=“2.16.840.1.113883.6.21”/>
<playingEntity classCode=“ENT”>
<name>...</name>
</playingEntity>
<scopingEntity classCode=“ENT”>
<name>...</name>
</scopingEntity>
</participant>
</participant>
<sourceOf typeCode=“REL”>
<target classCode=“ACT”>
<id root=“1.3.6.1.4.1.12009.3” extension=“A1235”/>
</target>
</sourceOf>
</act>
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Refined Model – Observation on Patient
Organization
classCode *: <= OR G
de te r m ine r Code *: <= INSTANCE
name: BAG<EN> [0..*]
standardIndustryClassCode: CE CWE [0..1]
<= OrganizationIndustryClass
0..1 providerOrganization
0..* patient
Patient
classCode *: <= PAT
0..* patient
id: SET<II> [0..*]
subject
code: CE CWE [0..1] <= RoleCode
addr: BAG<AD> [0..*]
type Code *: <= SBJ
telecom: BAG<TEL> [0..*]
awarenessCode: CE CWE [0..1] <= TargetAwareness
statusCode: SET<CS> CNE [0..*] <= RoleStatus
effectiveTime: IVL<TS> [0..1]
confidentialityCode: CE CWE [0..1] <= Confidentiality
veryImportantPersonCode: CE CWE [0..1] <= PatientImportance 0..* healthCareProvider
ObservationEvent
classCode *: <= OBS
m oodCode *: <= EVN
id*: II [1..1]
code*: CD CWE [1..1] <= Ob servationType
text: ED [0..1]
statusCode*: CS CNE [1..1] <= completed
effectiveTime*: IVL<TS> [1..1]
confidentialityCode: SET<CE> CWE [0..*] <= Confidentiality
component
type Code *: <= C OMP 0..* observationEvent
0..1 patientPerson
Person
ObservationEvent
classCode *: <= PSN
de te r m ine r Code *: <= INSTANCE
id: SET<II> [0..*]
code: CE CWE [0..1] <= EntityCode
name: BAG<EN> [0..*]
riskCode: CE CWE [0..1] <= EntityRisk
handlingCode: CE CWE [0..1] <= EntityHandling
administrativeGenderCode: CE CWE [0..1] <= AdministrativeGender
birthTime: TS [0..1]
deceasedTime: TS [0..1]
maritalStatusCode: CE CWE [0..1] <= MaritalStatus
educationLevelCode: CE CWE [0..1] <= EducationLevel
disabilityCode: SET<CE> CWE [0..*] <= PersonDisab ilityType
livingArrangementCode: CE CWE [0..1] <= LivingArrangement
religiousAffiliationCode: CE CWE [0..1] <= ReligiousAffiliation
raceCode: SET<CE> CWE [0..*] <= Race
ethnicGroupCode: SET<CE> CWE [0..*] <= Ethnicity
classCode *: <= OBS
m oodCode *: <= EVN
id*: II [1..1]
code*: CD CWE [1..1] <= Ob servationType
statusCode: CS CNE [1..1] <= completed
effectiveTime*: IVL<TS> [0..1]
confidentialityCode: SET<CE> CWE [0..*] <= Confidentiality
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Observation on Patient in XML
<observationEvent classCode=“OBS” moodCode=“EVN”>
<id root=“1.3.6.1.4.1.12009.3” extension=“A1234”/>
<code code=“...” codeSystem=“2.16.840.1.113883.6.1”/>
<subject typeCode=“…”>
<patient classCode=“ROL”>
<id root=“1.3.6.1.4.1.12009.4” extension=“1234567-8”/>
<code code=“…” codeSystem=“2.16.840.1.113883.6.21”/>
<patientPerson classCode=“PSN”>
<name><given>John</given><family>Doe</family></name>
</patientPerson>
<providerOrganization classCode=“ORG”>
<name>St., Josephs Hospital</name>
</providerOrganization>
</patient>
</subject>
<component typeCode=“REL”>
<observationEvent classCode=“ACT”>
<id root=“1.3.6.1.4.1.12009.3” extension=“A1235”/>
</observationEvent>
</component>
</observationEvent>
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Refined Model – Observation on Trial Subject
Organization
classCode *: <= OR G
de te r m ine r Code *: <= INSTANCE
name: BAG<EN> [0..*]
standardIndustryClassCode: CE CWE [0..1]
<= OrganizationIndustryClass
0..1 researchSponsor
ObservationEvent
0..* sponsoredSubject
ResearchSubject
classCode *: <= RESBJ
0..* researchSubject
id: SET<II> [0..*]
subject
code: CE CWE [0..1] <= RoleCode
type Code *: <= SBJ
addr: BAG<AD> [0..*]
telecom: BAG<TEL> [0..*]
statusCode: SET<CS> CNE [0..*] <= RoleStatus
effectiveTime: IVL<TS> [0..1]
0..* subjectOf
classCode *: <= OBS
m oodCode *: <= EVN
id*: II [1..1]
code*: CD CWE [1..1] <= Ob servationType
text: ED [0..1]
statusCode*: CS CNE [1..1] <= completed
effectiveTime*: IVL<TS> [1..1]
confidentialityCode: SET<CE> CWE [0..*] <= Confidentiality
component
type Code *: <= C OMP
0..* observationEvent
0..1 subjectPerson
Person
ObservationEvent
classCode *: <= PSN
de te r m ine r Code *: <= INSTANCE
id: SET<II> [0..*]
code: CE CWE [0..1] <= EntityCode
name: BAG<EN> [0..*]
riskCode: CE CWE [0..1] <= EntityRisk
handlingCode: CE CWE [0..1] <= EntityHandling
administrativeGenderCode: CE CWE [0..1] <= AdministrativeGender
birthTime: TS [0..1]
deceasedTime: TS [0..1]
maritalStatusCode: CE CWE [0..1] <= MaritalStatus
educationLevelCode: CE CWE [0..1] <= EducationLevel
disabilityCode: SET<CE> CWE [0..*] <= PersonDisab ilityType
livingArrangementCode: CE CWE [0..1] <= LivingArrangement
religiousAffiliationCode: CE CWE [0..1] <= ReligiousAffiliation
raceCode: SET<CE> CWE [0..*] <= Race
ethnicGroupCode: SET<CE> CWE [0..*] <= Ethnicity
classCode *: <= OBS
m oodCode *: <= EVN
id*: II [1..1]
code*: CD CWE [1..1] <= Ob servationType
statusCode: CS CNE [1..1] <= completed
effectiveTime*: IVL<TS> [0..1]
confidentialityCode: SET<CE> CWE [0..*] <= Confidentiality
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Observation on Trial Subject in XML
<observationEvent classCode=“OBS” moodCode=“EVN”>
<id root=“1.3.6.1.4.1.12009.3” extension=“A1234”/>
<code code=“...” codeSystem=“2.16.840.1.113883.6.1”/>
<subject typeCode=“…”>
<researchSubject classCode=“ROL”>
<id root=“1.3.6.1.4.1.12009.5” extension=“1234567-8”/>
<code code=“…” codeSystem=“2.16.840.1.113883.6.21”/>
<subjectPerson classCode=“PSN”>
<name><given>John</given><family>Doe</family></name>
</subjectPerson>
<researchSponsor classCode=“ORG”>
<name>Eli Lilly</name>
</researchSponsor>
</researchSubject>
</subject>
<component typeCode=“REL”>
<observationEvent classCode=“ACT”>
<id root=“1.3.6.1.4.1.12009.3” extension=“A1235”/>
</observationEvent>
</component>
</observationEvent>
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Data Types for Biomedical
Information
• Medical information needs more than just
string, int and float.
• Coded data: code, codeSystem,
displayName, originalText.
• Measurement values (physical quantities)
value and unit.
• Incomplete information (null flavors): not
applicable, unknown, vs. not asked.
• Uncertain values with probabilities and
distributions, aggregate distribution data.
• Correlated data series, time series,
multidimensional data.
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Current Applications of HL7 v3
• Traditional individual health care
• New Frontiers:
•
•
•
•
Laboratory Automation
Veterinary medicine (AVMA)
Public health (CDC’s PHDM)
Food and Drug Safety (FDA)
• Clinical Trials Reporting (FDA, CDISC)
• Chemical Stability Testing (FDA)
• Adverse Event Reporting (FDA, E2BM)
• Clinical Genomics
• Implantable Devices – Cardiology
• Patient Safety
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Advantages of HL7 and the RIM
• make data more consistent and
comparable
• reduce differences at overlaps
between specialty standards
• common data-patterns for common
problems
• highly flexible and deep model of
medical information
• minimize cost of data collection by
tapping into existing data streams
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HL7 for Biomedical Research
• Regulated Clinical Research
Information Management
Technical Committee (RCRIM)
• Clinical Genomics Special
Interest Group (CG SIG)
• Orders and Observations
Technical Committee
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R Clinical Research IM TC
• Clinical trials related medical
information
• Clinical trials protocols
specification framework
• Surveillance, product labeling,
regulatory documents
• Collaborative with industry and
government (e.g., Lilly, FDA,
CDISC)
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Clinical Genomics SIG
• support application of genomics
in clinical medicine
• specify use-cases and data
requirements
• review existing genomics
specifications
• recommend enhancements to
HL7 standards to support
genomics
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HL7Clinical GenomicsSIG
Document:
Subject:
Authors:
Individual Genotype DIM (to be used as a CMET or similar mechanism)
Genomics Data
Rev:
0.4
Date:
September 12, 2003
Amnon Shabo (IBM Research in Haifa), Shosh Israel (Hadassah University Hospital)
CGSIG
(CGEN_RM000002)
Note:
Clinical-Genomics
Entry point to the
Genotype Model
This IndividualAllele is a shadow and
together with the main one, both alleles
represent the allele pair on the paternal
and maternal chromosomes.
SNP_Haplotype
classCode *: <= OBS
m oodCode *: <= EVN
id: II [0..1]
code: CE CWE
classCode *: <= ACT
m oodCode *: <= EVN
id: II [0..1]
code: CE CWE
(haplotype identifier and
classification, e.g.,
Entrez)
0..* sNP_Haplotype
componentOf
Note:
A related allele that is on a
different haplotype, and still
has significant interrelation
with the source allele.
(could be attached to itself
recursively)
Haplotype
type Code *: <= C OMP
componentOf
Genotype
0..1 individualAllele
classCode *: <= OBS
m oodCode *: <= EVN
id: II [0..1]
code: CE CWE (e.g., HETEROZYGOTE)
text: ED
IndividualAllele
component1
type Code *: <= C OMP
component2
component3
type Code *: <= C OMP
type Code *: <= C OMP
0..* haplotype
type Code *: <= C OMP
DeterminantPeptide
IndividualAllele
pertinentInformation5
classCode *: <= OBS
m oodCode *: <= EVN
id: II [0..1]
code: CE CWE
(identifier and classification of the
determinant, e.g., Entrez)
text: ED
0..* pertinentIndividualAllele
type Code *: <= PERT
pertinentInformation2
0..*pertinentDeterminantPeptide
Note:
Use methodCode if
you don’t use the
associated method
procedure.
type Code *: <= PERT
SNP
AlleleSequence
1..1 individualAllele
classCode *: <= OBS
0..* pertinentSNP
m oodCode *: <= EVN
IndividualAllele
pertinentInformation1 classCode *: <= OBS
id: II [0..1]
code: CE CWE
type Code *: <= PERT
m oodCode *: <= EVN
(SNP identifier & classification, e.g.
code*: CE CWE [1..1]
Entrez dbSNP)
(allele identifier & classification, e.g. GeneBank)
text: ED
text: ED
value: ANY [0..1] (the SNP itself)
pertinentInformation3
pertinentInformation4
methodCode:SET<CE>CWE
type Code *: <= PERT
type Code *: <= PERT
Method
classCode *: <= OBS
m oodCode *: <= EVN
id: 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 sequencing
0..1 individualAllele method)
0..1 pertinentAlleleSequence
pertinentInformation2
type Code *: <= PERT
pertinentInformation
type Code *: <= PERT
classCode *: <= PROC
m oodCode *: <= EVN
id: II [0..1]
0..* pertinentMethod
code: CD CWE [0..1] <=
pertinentInformation1
ActCode
type Code *: <= PERT
(type of method)
text: ED [0..1]
(free text description of the
method used)
methodCode:SET<CE>CWE
[0..*]
outcome
IndividualAllele
0..* pertinentMutation
type Code *: <= OUTC
Mutation
classCode *: <= OBS
m oodCode *: <= EVN
0..1 pertinentGeneExpressionid: II [0..1]
code: CE CWE
(mutation identifier and
classification,
e.g. LOINC MOLECULAR
GENETICSNAMING)
text:
0..1 pertinentMutation
Mutation
GeneExpression
0..* pertinentMethod
Method
pertinentInformation
type Code *: <= PERT
classCode *: <= OBS
m oodCode *: <= EVN
id: 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..*]
type Code *: <= SEQL
0..* priorClinicalPhenotype
Constrained to a restricted MAGE-ML
content model, specified elesewhere.
0..* priorClinicalPhenotype
sequelTo
type Code *: <= SEQL
0..* priorClinicalPhenotype
SNP_Haplotype
Note:
The third allele is optional
and could be present if the
patient has three copies of
a chromosome as in the
Down’s Syndrome.
sequelTo
Constraint: GeneExpression.value
Genotype
0..* outcomePolypeptide
sequelTo
type Code *: <= SEQL
Polypeptide
classCode *: <= OBS
m oodCode *: <= EVN
id: II [0..1]
code*: CE CWE [1..1]
(idnetifier & classification of
the protein, e.g., SwissProt, )
(PDB, PIR, HUPO)
text:
Note:
An observation of a clinical condition
represented internally in this model.
Constraint: AlleleSequence.value
Constrained to a restricted
BSML or GMS content model,
specifiedelsewhere.
Note:
Usually this is a computed outcome, i.e.,
the lab does not produce the actual
protein.
ClinicalPhenotype
classCode *: <= OBS
m oodCode *: <= EVN
id: 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]
0..* priorClinicalPhenotype
DeterminantPeptide
sequelTo
type Code *: <= SEQL
reference
type Code *: <= x_ActRelationshipExternalReference
Note:
Could refine ActRelationship typeCode
to elaborate on different types of genomic
to phenotype effects.
11/10/2002
0..* referredToExternalClinicalPhenotype
ExternalClinicalPhenotype
classCode *: <= OBS
m oodCode *: <= EVN
id*: II [1..1]
(The id of an external observation (e.g., in a problem
list)
Note:
An external observation is a valid Observation
instance existing in any other HL7-compliant
artifact, e.g., a document or a message.
Copyright (c) 1999-2002 Regenstrief Institute for Health Care
Note: Shadowed observations
are copies of other
observations and thus have all
of the original act attributes.
22
HL7 CT SIG and other
Specifications in Bioinformatics
• CT SIG understands that there exist other
specifications in the field:
• Bioinformatic Sequence Markup Language (BSML)
• Microarray Gene Expression Markup Language
(MAGE-ML)
• Interoperable Informatics Infrastructure
Consortium (I3C)
• Systems Biology Markup Language (SBML)
• CellML, BioML, MoDL …
• There is significant overlap between those,
which one should one pick?
• It’s easy to make an XML schema for a
special purpose, but how does it integrate?
11/10/2002
Copyright (c) 1999-2002 Regenstrief Institute for Health Care
23
Myths and Facts about HL7
• HL7 is only about EDI
messaging in hospitals
• Must pay royalties to
use the HL7
specifications
• Must be a member to
use the HL7
specifications
• Must be a member to
participate in
development
11/10/2002
• HL7 develops
information models
• Final specification must
be purchased, no fee
for use
• No fee for use
• HL7 invites all
stakeholders to
participate
• Members can vote,
membership open to
anyone
Copyright (c) 1999-2002 Regenstrief Institute for Health Care
24
Take-Home Points
• Data integration problem is not
technological but conceptual
• Making a special XML schema is easy
• With HL7 you think integrated across
specialty applications
• Unlikely that clinical research needs
require special technology
• The general model facilitates
harmonization and interoperability
• HL7 has what it takes, work with it
11/10/2002
Copyright (c) 1999-2002 Regenstrief Institute for Health Care
25
thank you
Gunther Schadow,
Regenstrief Institute, Inc.
1050 Wishard Blvd.
Indianapolis, IN 46202
[email protected]
11/10/2002
Copyright (c) 1999-2002 Regenstrief Institute for Health Care
26