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A Standard-based Approach for Knowledge Representation MIE Oslo Norway, Aug 2011 Oral Presentation Ariel Farkash, Hani Neuvirth, Yaara Goldschmidt, Amnon Shabo IBM Haifa Research Lab, Israel Costanza Conti IMS-Istituto di Management

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MIE – Oslo Norway, Aug 2011

A Standard-based Approach for Knowledge Representation

Oral Presentation Ariel Farkash, Hani Neuvirth, Yaara Goldschmidt, Amnon Shabo – IBM Haifa Research Lab, Israel Costanza Conti – IMS-Istituto di Management

Sanitario SRL, Italy

Federica Rizzi – KOS Genetic SRL, Italy Stefano Bianchi – Softeco Sismat SRL, Italy Erika Salvi, Daniele Cusi – Hypergenes Consortium,

Fondazione Filaterete, Italy

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Haifa Research Lab

Some Terminology § Data – The raw clinical or genomic patient data § Knowledge – An understanding of the studied disease

that is not specific to any patient

§ Knowledge may publically available § Knowledge may be generated within the project scope e.g. analysis

  • n data

§ Information – a subject-specific analysis result that

can be used as a prediction or for decision support purposes

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Haifa Research Lab

WE WE US USE CDA CDA

Dealing with data…

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Haifa Research Lab

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0..1 assignedPerson 0..1 representedOrganization AssignedEntity Place classCode*: <= PLC determinerCode*: <= INSTANCE name: EN [0..1] addr: AD [0..1] 0..1 location 0..1 serviceProviderOrganization HealthCareFacility classCode*: <= SDLOC id: SET<II> [0..*] code: CE CWE [0..1] <= ServiceDeliveryLocationRoleType 1..1 representedCustodianOrganization AssignedCustodian classCode*: <= ASSIGNED 0..1 associatedPerson 0..1 scopingOrganization AssociatedEntity classCode*: <= RoleClassAssociative id: SET<II> [0..*] code: CE CWE [0..1] <= RoleCode addr: SET<AD> [0..*] telecom: SET<TEL> [0..*] 0..1 informationRecipient 0..1 receivedOrganization IntendedRecipient classCode*: <= x_InformationRecipientRole id*: SET<II> [0..*] addr: SET<AD> [0..*] telecom: SET<TEL> [0..*] 0..* serviceEvent typeCode*: <= DOC documentationOf 0..1 encompassingEncounter typeCode*: <= COMP componentOf 0..* parentDocument typeCode*: <= x_ActRelationshipDocument relatedDocument 0..1 assignedEntity typeCode*: <= RESP responsibleParty 0..* associatedEntity participant typeCode*: <= ParticipationType functionCode: CE CWE [0..1] <= ParticipationFunction contextControlCode*: CS CNE [1..1] <= "OP" time: IVL<TS> [0..1] 1..1 assignedCustodian typeCode*: <= CST custodian 0..* intendedRecipient typeCode*: <= x_InformationRecipient informationRecipient 0..* assignedEntity encounterParticipant typeCode*: <= x_EncounterParticipant time: IVL<TS> [0..1] 0..1 assignedEntity legalAuthenticator typeCode*: <= LA contextControlCode*: CS CNE [1..1] <= "OP" time*: TS [1..1] signatureCode*: CS CNE [1..1] <= ParticipationSignature 0..* assignedEntity authenticator typeCode*: <= AUTHEN time*: TS [1..1] signatureCode*: CS CNE [1..1] <= ParticipationSignature 1..* assignedAuthor author typeCode*: <= AUT functionCode: CE CWE [0..1] <= ParticipationFunction contextControlCode*: CS CNE [1..1] <= "OP" time*: TS [1..1] 1..* patientRole recordTarget typeCode*: <= RCT contextControlCode*: CS CNE [1..1] <= "OP" 0..1 healthCareFacility typeCode*: <= LOC location CDA R-MIM (POCD_RM000040) This RMIM is used to generate the CDA specification. 1..1 bodyChoice component typeCode*: <= COMP contextConductionInd*: BL [1..1] "true" component 0..* section typeCode*: <= COMP contextConductionInd*: BL [1..1] "true" 0..* clinicalStatement entry typeCode*: <= x_ActRelationshipEntry contextConductionInd*: BL [1..1] "true" Section classCode*: <= DOCSECT moodCode*: <= EVN id: II [0..1] code: CE CWE [0..1] <= DocumentSectionType title: ST [0..1] text*: ED [0..1] confidentialityCode: CE CWE [0..1] <= x_BasicConfidentialityKind languageCode: CS CNE [0..1] <= HumanLanguage StructuredBody classCode*: <= DOCBODY moodCode*: <= EVN confidentialityCode: CE CWE [0..1] <= x_BasicConfidentialityKind languageCode: CS CNE [0..1] <= HumanLanguage NonXMLBody classCode*: <= DOCBODY moodCode*: <= EVN text: ED [1..1] confidentialityCode: CE CWE [0..1] <= x_BasicConfidentialityKind languageCode: CS CNE [0..1] <= HumanLanguage ParentDocument classCode*: <= DOCCLIN moodCode*: <= EVN id*: SET<II> [1..*] code: CD CWE [0..1] <= DocumentType text: ED [0..1] setId: II [0..1] versionNumber: INT [0..1] ClinicalDocument classCode*: <= DOCCLIN moodCode*: <= EVN id*: II [1..1] code*: CE CWE [1..1] <= DocumentType title: ST [0..1] effectiveTime*: TS [1..1] confidentialityCode*: CE CWE [1..1] <= x_BasicConfidentialityKind languageCode: CS CNE [0..1] <= HumanLanguage setId: II [0..1] versionNumber: INT [0..1] copyTime: TS [0..1] (Deprecated) EncompassingEncounter classCode*: <= ENC moodCode*: <= EVN id: SET<II> [0..*] code: CE CWE [0..1] <= ActEncounterCode effectiveTime*: IVL<TS> [1..1] dischargeDispositionCode: CE CWE [0..1] <= EncounterDischargeDisposition bodyChoice 1..* section component typeCode*: <= COMP contextConductionInd*: BL [1..1] "true" 0..* informantChoice typeCode*: <= INF contextControlCode*: CS CNE [1..1] <= "OP" informant Section.text.mediaType fixed as "text/x-hl7-text+xml". See section "Section Narrative Block" for details. Constraint: Section.text 0..* order typeCode*: <= FLFS inFulfillmentOf Order classCode*: <= ACT moodCode*: <= RQO id*: SET<II> [1..*] code: CE CWE [0..1] <= ActCode priorityCode: CE CWE [0..1] <= ActPriority 0..1 relatedPerson RelatedEntity classCode*: <= RoleClassMutualRelationship code: CE CWE [0..1] <= PersonalRelationshipRoleType addr: SET<AD> [0..*] telecom: SET<TEL> [0..*] effectiveTime: IVL<TS> [0..1] CustodianOrganization classCode*: <= ORG determinerCode*: <= INSTANCE id*: SET<II> [1..*] name: ON [0..1] telecom: TEL [0..1] addr: AD [0..1] 0..1 patient 0..1 providerOrganization PatientRole classCode*: <= PAT id: SET<II> [1..*] addr: SET<AD> [0..*] telecom: SET<TEL> [0..*] Patient classCode*: <= PSN determinerCode*: <= INSTANCE id: II [0..1] (Deprecated) name: SET<PN> [0..*] administrativeGenderCode: CE CWE [0..1] <= AdministrativeGender birthTime: TS [0..1] maritalStatusCode: CE CWE [0..1] <= MaritalStatus religiousAffiliationCode: CE CWE [0..1] <= ReligiousAffiliation raceCode: CE CWE [0..1] <= Race ethnicGroupCode: CE CWE [0..1] <= Ethnicity 0..1 assignedAuthorChoice 0..1 representedOrganization AssignedAuthor classCode*: <= ASSIGNED id*: SET<II> [1..*] code: CE CWE [0..1] <= RoleCode addr: SET<AD> [0..*] telecom: SET<TEL> [0..*] Person classCode*: <= PSN determinerCode*: <= INSTANCE name: SET<PN> [0..*] Organization Organization Organization Organization Organization 0..1 subject 0..1 RelatedSubject classCode*: <= x_DocumentSubject code: CE CWE [0..1] <= PersonalRelationshipRoleType addr: SET<AD> [0..*] telecom: SET<TEL> [0..*] SubjectPerson classCode*: <= PSN determinerCode*: <= INSTANCE name: SET<PN> [0..*] administrativeGenderCode: CE CWE [0..1] <= AdministrativeGender birthTime: TS [0..1] AuthoringDevice classCode*: <= DEV determinerCode*: <= INSTANCE code: CE CWE [0..1] <= EntityCode manufacturerModelName: SC CWE [0..1] <= ManufacturerModelName softwareName: SC CWE [0..1] <= SoftwareName AuthorChoice 1..1 maintainingPerson MaintainedEntity 0..* asMaintainedEntity classCode*: <= MNT effectiveTime: IVL<TS> [0..1] Person 0..1 assignedPerson 0..1 representedOrganization AssignedEntity classCode*: <= ASSIGNED id*: SET<II> [1..*] code: CE CWE [0..1] <= RoleCode addr: SET<AD> [0..*] telecom: SET<TEL> [0..*] Person 1..1 guardianChoice Guardian 0..* guardian classCode*: <= GUARD id: SET<II> [0..*] code: CE CWE [0..1] <= RoleCode addr: SET<AD> [0..*] telecom: SET<TEL> [0..*] Organization Person GuardianChoice Consent classCode*: <= CONS moodCode*: <= EVN id: SET<II> [0..*] code: CE CWE [0..1] <= ActCode statusCode*: CS CNE [1..1] <= completed 0..* consent typeCode*: <= AUTH authorization 0..1 relatedSubject typeCode*: <= SBJ contextControlCode*: CS CNE [1..1] <= "OP" awarenessCode: CE CWE [0..1] <= TargetAwareness subject 0..* informant 0..* author 0..1 assignedEntity dataEnterer typeCode*: <= ENT (Transcriptionist) contextControlCode*: CS CNE [1..1] <= "OP" time: TS [0..1] 0..1 assignedPerson 0..1 representedOrganization AssignedEntity 1..1 place Birthplace 0..1 birthplace classCode*: <= BIRTHPL LanguageCommunication (LanguageCommunication) languageCode: CS CNE [0..1] <= HumanLanguage modeCode: CE CWE [0..1] <= LanguageAbilityMode proficiencyLevelCode: CE CWE [0..1] <= LanguageAbilityProficiency preferenceInd: BL [0..1] 0..* languageCommunication Person Person Place informantChoice 0..1 assignedPerson 0..1 representedOrganization AssignedEntity Person 0..* externalActChoice typeCode*: <= x_ActRelationshipExternalReference seperatableInd: BL [0..1] reference Observation classCode*: <= OBS moodCode*: <= x_ActMoodDocumentObservation id: SET<II> [0..*] code*: CD CWE [1..1] <= ObservationType negationInd: BL [0..1] derivationExpr: ST [0..1] text: ED [0..1] statusCode: CS CNE [0..1] <= ActStatus effectiveTime: IVL<TS> [0..1] priorityCode: CE CWE [0..1] <= ActPriority repeatNumber: IVL<INT> [0..1] languageCode: CS CNE [0..1] <= HumanLanguage value: ANY [0..1] interpretationCode: SET<CE> CNE [0..*] methodCode: SET<CE> CWE [0..*] targetSiteCode: SET<CD> CWE [0..*] ObservationMedia classCode*: <= OBS moodCode*: <= EVN id: SET<II> [0..*] languageCode: CS CNE [0..1] <= HumanLanguage value*: ED [1..1] RegionOfInterest classCode*: <= ROIOVL moodCode*: <= EVN id*: SET<II> [1..*] code*: CS CNE [1..1] <= ROIOverlayShape value*: LIST<INT> [1..*] SubstanceAdministration classCode*: <= SBADM moodCode*: <= x_DocumentSubstanceMood id: SET<II> [0..*] code: CD CWE [0..1] <= SubstanceAdministrationActCode negationInd: BL [0..1] text: ED [0..1] statusCode: CS CNE [0..1] <= ActStatus effectiveTime: GTS [0..1] priorityCode: CE CWE [0..1] <= ActPriority repeatNumber: IVL<INT> [0..1] routeCode: CE CWE [0..1] <= RouteOfAdministration approachSiteCode: SET<CD> CWE [0..*] <= ActSite doseQuantity: IVL<PQ> [0..1] rateQuantity: IVL<PQ> [0..1] maxDoseQuantity: RTO<PQ,PQ> [0..1] administrationUnitCode: CE CWE [0..1] <= AdministrableDrugForm Supply classCode*: <= SPLY moodCode*: <= x_DocumentSubstanceMood id: SET<II> [0..*] code: CD CWE [0..1] <= ActCode text: ED [0..1] statusCode: CS CNE [0..1] <= ActStatus effectiveTime: GTS [0..1] priorityCode: SET<CE> CWE [0..*] <= ActPriority repeatNumber: IVL<INT> [0..1] independentInd: BL [0..1] quantity: PQ [0..1] expectedUseTime: IVL<TS> [0..1] Procedure classCode*: <= PROC moodCode*: <= x_DocumentProcedureMood id: SET<II> [0..*] code: CD CWE [0..1] negationInd: BL [0..1] text: ED [0..1] statusCode: CS CNE [0..1] <= ActStatus effectiveTime: IVL<TS> [0..1] priorityCode: CE CWE [0..1] <= ActPriority languageCode: CS CNE [0..1] <= HumanLanguage methodCode: SET<CE> CWE [0..*] approachSiteCode: SET<CD> CWE [0..*] targetSiteCode: SET<CD> CWE [0..*] ExternalAct classCode*: <= ACT moodCode*: <= EVN id: SET<II> [0..*] code: CD CWE [0..1] <= ActCode text: ED [0..1] ExternalObservation classCode*: <= OBS moodCode*: <= EVN id: SET<II> [0..*] code: CD CWE [0..1] <= ActCode text: ED [0..1] ExternalProcedure classCode*: <= PROC moodCode*: <= EVN id: SET<II> [0..*] code: CD CWE [0..1] <= ActCode text: ED [0..1] externalActChoice clinicalStatement entryRelationship 0..* clinicalStatement typeCode*: <= x_ActRelationshipEntryRelationship inversionInd: BL [0..1] contextConductionInd*: BL [1..1] "true" sequenceNumber: INT [0..1] negationInd: BL [0..1] seperatableInd: BL [0..1] 1..1 manufacturedProduct consumable typeCode*: <= CSM 0..* criterion typeCode*: <= PRCN precondition Criterion classCode*: <= OBS moodCode*: <= EVN.CRT code: CD CWE [0..1] <= ActCode text: ED [0..1] value: ANY [0..1] 1..1 manufacturedDrugOrOtherMaterial 0..1 manufacturerOrganization ManufacturedProduct classCode*: <= MANU id: SET<II> [0..*] Encounter classCode*: <= ENC moodCode*: <= x_DocumentEncounterMood id: SET<II> [0..*] code: CD CWE [0..1] <= ActEncounterCode text: ED [0..1] statusCode: CS CNE [0..1] <= ActStatus effectiveTime: IVL<TS> [0..1] priorityCode: CE CWE [0..1] <= ActPriority 0..1 playingEntityChoice 0..1 scopingEntity ParticipantRole classCode*: <= ROL id: SET<II> [0..*] code: CE CWE [0..1] <= RoleCode addr: SET<AD> [0..*] telecom: SET<TEL> [0..*] PlayingEntity classCode*: <= ENT determinerCode*: <= INSTANCE code: CE CWE [0..1] <= EntityCode quantity: SET<PQ> [0..*] name: SET<PN> [0..*] desc: ED [0..1] Entity classCode*: <= ENT determinerCode*: <= INSTANCE id: SET<II> [0..*] code: CE CWE [0..1] <= EntityCode desc: ED [0..1] Device classCode*: <= DEV determinerCode*: <= INSTANCE code: CE CWE [0..1] <= EntityCode manufacturerModelName: SC CWE [0..1] <= ManufacturerModelName softwareName: SC CWE [0..1] <= SoftwareName EntityChoice ExternalDocument classCode*: <= DOC moodCode*: <= EVN id: SET<II> [0..*] code: CD CWE [0..1] <= DocumentType text: ED [0..1] setId: II [0..1] versionNumber: INT [0..1] 0..* informant 0..* author 0..1 subject 0..* participantRole typeCode*: <= ParticipationType contextControlCode*: CS CNE [1..1] <= "OP" time: IVL<TS> [0..1] awarenessCode: CE CWE [0..1] <= TargetAwareness participant 0..* assignedEntity performer typeCode*: <= PRF time: IVL<TS> [0..1] modeCode: CE CWE [0..1] <= ParticipationMode 0..1 assignedPerson 0..1 representedOrganization AssignedEntity 0..* observationRange typeCode*: <= REFV referenceRange ObservationRange classCode*: <= OBS moodCode*: <= EVN.CRT code: CD CWE [0..1] <= ActCode text: ED [0..1] value: ANY [0..1] interpretationCode: CE CNE [0..1] <= ObservationInterpretation Organizer classCode*: <= x_ActClassDocumentEntryOrganizer moodCode*: <= EVN id: SET<II> [0..*] code: CD CWE [0..1] <= ActCode statusCode*: CS CNE [1..1] <= ActStatus effectiveTime: IVL<TS> [0..1] The Organizer clone can be the source
  • f the component relationship or
the reference relationship, but not the entryRelationship relationship. Constraint: Organizer Act classCode*: <= x_ActClassDocumentEntryAct moodCode*: <= x_DocumentActMood id: SET<II> [0..*] code*: CD CWE [1..1] <= ActCode negationInd: BL [0..1] text: ED [0..1] statusCode: CS CNE [0..1] <= ActStatus effectiveTime: IVL<TS> [0..1] priorityCode: CE CWE [0..1] <= ActPriority languageCode: CS CNE [0..1] <= HumanLanguage 0..1 manufacturedProduct * typeCode*: <= PRD product Material classCode*: <= MMAT determinerCode*: <= KIND code: CE CWE [0..1] <= MaterialEntityClassType name: EN [0..1] lotNumberText: ST [0..1] LabeledDrug classCode*: <= MMAT determinerCode*: <= KIND code: CE CWE [0..1] <= DrugEntity name: EN [0..1] DrugOrOtherMaterial Organization classCode*: <= ORG determinerCode*: <= INSTANCE id: SET<II> [0..*] name: SET<ON> [0..*] telecom: SET<TEL> [0..*] addr: SET<AD> [0..*] standardIndustryClassCode: CE CWE [0..1] <= OrganizationIndustryClass 0..* specimenRole typeCode*: <= SPC specimen 0..1 specimenPlayingEntity SpecimenRole classCode*: <= SPEC id: SET<II> [0..*] Organization ParentDocument.text can be used to indicate the MIME type of the related document. It is not to be used to embed the related document, and thus ParentDocument.text.BIN is precluded from use. Constraint: ParentDocument.text ServiceEvent classCode*: <= ACT moodCode*: <= EVN id: SET<II> [0..*] code: CE CWE [0..1] effectiveTime: IVL<TS> [0..1] 0..* assignedEntity performer typeCode*: <= x_ServiceEventPerformer functionCode: CE CWE [0..1] <= ParticipationFunction time: IVL<TS> [0..1] 0..1 assignedPerson 0..1 representedOrganization AssignedEntity A conformant CDA document can have a single relatedDocument with typeCode "APND"; a single relatedDocument with typeCode "RPLC"; a single relatedDocument with typeCode "XFRM"; two relatedDocuments with typeCodes "XFRM" and "RPLC"; or two relatedDocuments with typeCodes "XFRM" and "APND". Constraint: relatedDocument.typeCode 0..1 wholeOrganization OrganizationPartOf 0..1 asOrganizationPartOf classCode*: <= PART id*: SET<II> [0..*] code: CE CWE [0..1] <= RoleCode statusCode: CS CNE [0..1] <= RoleStatus effectiveTime: IVL<TS> [0..1] Note: Observation.value has cardinality [0..*], which doesn't show up in the Visio representation. component 0..* clinicalStatement typeCode*: <= COMP contextConductionInd*: BL [1..1] "true" sequenceNumber: INT [0..1] seperatableInd: BL [0..1]

CDA Header CDA Body CDA Entries The Clinical Document Architecture (CDA) Release 2 Model

Clinical Documentation Participations

Non-XML or Structured Body Nested Sections w/ Narrative Clinical Statement Custodian Record Target Encounter

Related Documents

Referenced (HL7)

  • bjects

Medication

Recursive relation of Entries

Observation Procedure

Narrative Content Model

Ext. Ref.

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Haifa Research Lab

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HL7 Clinical Document Architecture (CDA)

Clinical Trials

0..1 assignedPerson 0..1 representedOrganization AssignedEntity Place classCode*: <= PLC determinerCode*: <= INSTANCE name: EN [0..1] addr: AD [0..1] 0..1 location 0..1 serviceProviderOrganization HealthCareFacility classCode*: <= SDLOC id: SET<II> [0..*] code: CE CWE [0..1] <= ServiceDeliveryLocationRoleType 1..1 representedCustodianOrganization AssignedCustodian classCode*: <= ASSIGNED 0..1 associatedPerson 0..1 scopingOrganization AssociatedEntity classCode*: <= RoleClassAssociative id: SET<II> [0..*] code: CE CWE [0..1] <= RoleCode addr: SET<AD> [0..*] telecom: SET<TEL> [0..*] 0..1 informationRecipient 0..1 receivedOrganization IntendedRecipient classCode*: <= x_InformationRecipientRole id*: SET<II> [0..*] addr: SET<AD> [0..*] telecom: SET<TEL> [0..*] 0..* serviceEvent typeCode*: <= DOC documentationOf 0..1 encompassingEncounter typeCode*: <= COMP componentOf 0..* parentDocument typeCode*: <= x_ActRelationshipDocument relatedDocument 0..1 assignedEntity typeCode*: <= RESP responsibleParty 0..* associatedEntity participant typeCode*: <= ParticipationType functionCode: CE CWE [0..1] <= ParticipationFunction contextControlCode*: CS CNE [1..1] <= "OP" time: IVL<TS> [0..1] 1..1 assignedCustodian typeCode*: <= CST custodian 0..* intendedRecipient typeCode*: <= x_InformationRecipient informationRecipient 0..* assignedEntity encounterParticipant typeCode*: <= x_EncounterParticipant time: IVL<TS> [0..1] 0..1 assignedEntity legalAuthenticator typeCode*: <= LA contextControlCode*: CS CNE [1..1] <= "OP" time*: TS [1..1] signatureCode*: CS CNE [1..1] <= ParticipationSignature 0..* assignedEntity authenticator typeCode*: <= AUTHEN time*: TS [1..1] signatureCode*: CS CNE [1..1] <= ParticipationSignature 1..* assignedAuthor author typeCode*: <= AUT functionCode: CE CWE [0..1] <= ParticipationFunction contextControlCode*: CS CNE [1..1] <= "OP" time*: TS [1..1] 1..* patientRole recordTarget typeCode*: <= RCT contextControlCode*: CS CNE [1..1] <= "OP" 0..1 healthCareFacility typeCode*: <= LOC location CDA R-MIM (POCD_RM000040) This RMIM is used to generate the CDA specification. 1..1 bodyChoice component typeCode*: <= COMP contextConductionInd*: BL [1..1] "true" component 0..* section typeCode*: <= COMP contextConductionInd*: BL [1..1] "true" 0..* clinicalStatement entry typeCode*: <= x_ActRelationshipEntry contextConductionInd*: BL [1..1] "true" Section classCode*: <= DOCSECT moodCode*: <= EVN id: II [0..1] code: CE CWE [0..1] <= DocumentSectionType title: ST [0..1] text*: ED [0..1] confidentialityCode: CE CWE [0..1] <= x_BasicConfidentialityKind languageCode: CS CNE [0..1] <= HumanLanguage StructuredBody classCode*: <= DOCBODY moodCode*: <= EVN confidentialityCode: CE CWE [0..1] <= x_BasicConfidentialityKind languageCode: CS CNE [0..1] <= HumanLanguage NonXMLBody classCode*: <= DOCBODY moodCode*: <= EVN text: ED [1..1] confidentialityCode: CE CWE [0..1] <= x_BasicConfidentialityKind languageCode: CS CNE [0..1] <= HumanLanguage ParentDocument classCode*: <= DOCCLIN moodCode*: <= EVN id*: SET<II> [1..*] code: CD CWE [0..1] <= DocumentType text: ED [0..1] setId: II [0..1] versionNumber: INT [0..1] ClinicalDocument classCode*: <= DOCCLIN moodCode*: <= EVN id*: II [1..1] code*: CE CWE [1..1] <= DocumentType title: ST [0..1] effectiveTime*: TS [1..1] confidentialityCode*: CE CWE [1..1] <= x_BasicConfidentialityKind languageCode: CS CNE [0..1] <= HumanLanguage setId: II [0..1] versionNumber: INT [0..1] copyTime: TS [0..1] (Deprecated) EncompassingEncounter classCode*: <= ENC moodCode*: <= EVN id: SET<II> [0..*] code: CE CWE [0..1] <= ActEncounterCode effectiveTime*: IVL<TS> [1..1] dischargeDispositionCode: CE CWE [0..1] <= EncounterDischargeDisposition bodyChoice 1..* section component typeCode*: <= COMP contextConductionInd*: BL [1..1] "true" 0..* informantChoice typeCode*: <= INF contextControlCode*: CS CNE [1..1] <= "OP" informant Section.text.mediaType fixed as "text/x-hl7-text+xml". See section "Section Narrative Block" for details. Constraint: Section.text 0..* order typeCode*: <= FLFS inFulfillmentOf Order classCode*: <= ACT moodCode*: <= RQO id*: SET<II> [1..*] code: CE CWE [0..1] <= ActCode priorityCode: CE CWE [0..1] <= ActPriority 0..1 relatedPerson RelatedEntity classCode*: <= RoleClassMutualRelationship code: CE CWE [0..1] <= PersonalRelationshipRoleType addr: SET<AD> [0..*] telecom: SET<TEL> [0..*] effectiveTime: IVL<TS> [0..1] CustodianOrganization classCode*: <= ORG determinerCode*: <= INSTANCE id*: SET<II> [1..*] name: ON [0..1] telecom: TEL [0..1] addr: AD [0..1] 0..1 patient 0..1 providerOrganization PatientRole classCode*: <= PAT id: SET<II> [1..*] addr: SET<AD> [0..*] telecom: SET<TEL> [0..*] Patient classCode*: <= PSN determinerCode*: <= INSTANCE id: II [0..1] (Deprecated) name: SET<PN> [0..*] administrativeGenderCode: CE CWE [0..1] <= AdministrativeGender birthTime: TS [0..1] maritalStatusCode: CE CWE [0..1] <= MaritalStatus religiousAffiliationCode: CE CWE [0..1] <= ReligiousAffiliation raceCode: CE CWE [0..1] <= Race ethnicGroupCode: CE CWE [0..1] <= Ethnicity 0..1 assignedAuthorChoice 0..1 representedOrganization AssignedAuthor classCode*: <= ASSIGNED id*: SET<II> [1..*] code: CE CWE [0..1] <= RoleCode addr: SET<AD> [0..*] telecom: SET<TEL> [0..*] Person classCode*: <= PSN determinerCode*: <= INSTANCE name: SET<PN> [0..*] Organization Organization Organization Organization Organization 0..1 subject 0..1 RelatedSubject classCode*: <= x_DocumentSubject code: CE CWE [0..1] <= PersonalRelationshipRoleType addr: SET<AD> [0..*] telecom: SET<TEL> [0..*] SubjectPerson classCode*: <= PSN determinerCode*: <= INSTANCE name: SET<PN> [0..*] administrativeGenderCode: CE CWE [0..1] <= AdministrativeGender birthTime: TS [0..1] AuthoringDevice classCode*: <= DEV determinerCode*: <= INSTANCE code: CE CWE [0..1] <= EntityCode manufacturerModelName: SC CWE [0..1] <= ManufacturerModelName softwareName: SC CWE [0..1] <= SoftwareName AuthorChoice 1..1 maintainingPerson MaintainedEntity 0..* asMaintainedEntity classCode*: <= MNT effectiveTime: IVL<TS> [0..1] Person 0..1 assignedPerson 0..1 representedOrganization AssignedEntity classCode*: <= ASSIGNED id*: SET<II> [1..*] code: CE CWE [0..1] <= RoleCode addr: SET<AD> [0..*] telecom: SET<TEL> [0..*] Person 1..1 guardianChoice Guardian 0..* guardian classCode*: <= GUARD id: SET<II> [0..*] code: CE CWE [0..1] <= RoleCode addr: SET<AD> [0..*] telecom: SET<TEL> [0..*] Organization Person GuardianChoice Consent classCode*: <= CONS moodCode*: <= EVN id: SET<II> [0..*] code: CE CWE [0..1] <= ActCode statusCode*: CS CNE [1..1] <= completed 0..* consent typeCode*: <= AUTH authorization 0..1 relatedSubject typeCode*: <= SBJ contextControlCode*: CS CNE [1..1] <= "OP" awarenessCode: CE CWE [0..1] <= TargetAwareness subject 0..* informant 0..* author 0..1 assignedEntity dataEnterer typeCode*: <= ENT (Transcriptionist) contextControlCode*: CS CNE [1..1] <= "OP" time: TS [0..1] 0..1 assignedPerson 0..1 representedOrganization AssignedEntity 1..1 place Birthplace 0..1 birthplace classCode*: <= BIRTHPL LanguageCommunication (LanguageCommunication) languageCode: CS CNE [0..1] <= HumanLanguage modeCode: CE CWE [0..1] <= LanguageAbilityMode proficiencyLevelCode: CE CWE [0..1] <= LanguageAbilityProficiency preferenceInd: BL [0..1] 0..* languageCommunication Person Person Place informantChoice 0..1 assignedPerson 0..1 representedOrganization AssignedEntity Person 0..* externalActChoice typeCode*: <= x_ActRelationshipExternalReference seperatableInd: BL [0..1] reference Observation classCode*: <= OBS moodCode*: <= x_ActMoodDocumentObservation id: SET<II> [0..*] code*: CD CWE [1..1] <= ObservationType negationInd: BL [0..1] derivationExpr: ST [0..1] text: ED [0..1] statusCode: CS CNE [0..1] <= ActStatus effectiveTime: IVL<TS> [0..1] priorityCode: CE CWE [0..1] <= ActPriority repeatNumber: IVL<INT> [0..1] languageCode: CS CNE [0..1] <= HumanLanguage value: ANY [0..1] interpretationCode: SET<CE> CNE [0..*] methodCode: SET<CE> CWE [0..*] targetSiteCode: SET<CD> CWE [0..*] ObservationMedia classCode*: <= OBS moodCode*: <= EVN id: SET<II> [0..*] languageCode: CS CNE [0..1] <= HumanLanguage value*: ED [1..1] RegionOfInterest classCode*: <= ROIOVL moodCode*: <= EVN id*: SET<II> [1..*] code*: CS CNE [1..1] <= ROIOverlayShape value*: LIST<INT> [1..*] SubstanceAdministration classCode*: <= SBADM moodCode*: <= x_DocumentSubstanceMood id: SET<II> [0..*] code: CD CWE [0..1] <= SubstanceAdministrationActCode negationInd: BL [0..1] text: ED [0..1] statusCode: CS CNE [0..1] <= ActStatus effectiveTime: GTS [0..1] priorityCode: CE CWE [0..1] <= ActPriority repeatNumber: IVL<INT> [0..1] routeCode: CE CWE [0..1] <= RouteOfAdministration approachSiteCode: SET<CD> CWE [0..*] <= ActSite doseQuantity: IVL<PQ> [0..1] rateQuantity: IVL<PQ> [0..1] maxDoseQuantity: RTO<PQ,PQ> [0..1] administrationUnitCode: CE CWE [0..1] <= AdministrableDrugForm Supply classCode*: <= SPLY moodCode*: <= x_DocumentSubstanceMood id: SET<II> [0..*] code: CD CWE [0..1] <= ActCode text: ED [0..1] statusCode: CS CNE [0..1] <= ActStatus effectiveTime: GTS [0..1] priorityCode: SET<CE> CWE [0..*] <= ActPriority repeatNumber: IVL<INT> [0..1] independentInd: BL [0..1] quantity: PQ [0..1] expectedUseTime: IVL<TS> [0..1] Procedure classCode*: <= PROC moodCode*: <= x_DocumentProcedureMood id: SET<II> [0..*] code: CD CWE [0..1] negationInd: BL [0..1] text: ED [0..1] statusCode: CS CNE [0..1] <= ActStatus effectiveTime: IVL<TS> [0..1] priorityCode: CE CWE [0..1] <= ActPriority languageCode: CS CNE [0..1] <= HumanLanguage methodCode: SET<CE> CWE [0..*] approachSiteCode: SET<CD> CWE [0..*] targetSiteCode: SET<CD> CWE [0..*] ExternalAct classCode*: <= ACT moodCode*: <= EVN id: SET<II> [0..*] code: CD CWE [0..1] <= ActCode text: ED [0..1] ExternalObservation classCode*: <= OBS moodCode*: <= EVN id: SET<II> [0..*] code: CD CWE [0..1] <= ActCode text: ED [0..1] ExternalProcedure classCode*: <= PROC moodCode*: <= EVN id: SET<II> [0..*] code: CD CWE [0..1] <= ActCode text: ED [0..1] externalActChoice clinicalStatement entryRelationship 0..* clinicalStatement typeCode*: <= x_ActRelationshipEntryRelationship inversionInd: BL [0..1] contextConductionInd*: BL [1..1] "true" sequenceNumber: INT [0..1] negationInd: BL [0..1] seperatableInd: BL [0..1] 1..1 manufacturedProduct consumable typeCode*: <= CSM 0..* criterion typeCode*: <= PRCN precondition Criterion classCode*: <= OBS moodCode*: <= EVN.CRT code: CD CWE [0..1] <= ActCode text: ED [0..1] value: ANY [0..1] 1..1 manufacturedDrugOrOtherMaterial 0..1 manufacturerOrganization ManufacturedProduct classCode*: <= MANU id: SET<II> [0..*] Encounter classCode*: <= ENC moodCode*: <= x_DocumentEncounterMood id: SET<II> [0..*] code: CD CWE [0..1] <= ActEncounterCode text: ED [0..1] statusCode: CS CNE [0..1] <= ActStatus effectiveTime: IVL<TS> [0..1] priorityCode: CE CWE [0..1] <= ActPriority 0..1 playingEntityChoice 0..1 scopingEntity ParticipantRole classCode*: <= ROL id: SET<II> [0..*] code: CE CWE [0..1] <= RoleCode addr: SET<AD> [0..*] telecom: SET<TEL> [0..*] PlayingEntity classCode*: <= ENT determinerCode*: <= INSTANCE code: CE CWE [0..1] <= EntityCode quantity: SET<PQ> [0..*] name: SET<PN> [0..*] desc: ED [0..1] Entity classCode*: <= ENT determinerCode*: <= INSTANCE id: SET<II> [0..*] code: CE CWE [0..1] <= EntityCode desc: ED [0..1] Device classCode*: <= DEV determinerCode*: <= INSTANCE code: CE CWE [0..1] <= EntityCode manufacturerModelName: SC CWE [0..1] <= ManufacturerModelName softwareName: SC CWE [0..1] <= SoftwareName EntityChoice ExternalDocument classCode*: <= DOC moodCode*: <= EVN id: SET<II> [0..*] code: CD CWE [0..1] <= DocumentType text: ED [0..1] setId: II [0..1] versionNumber: INT [0..1] 0..* informant 0..* author 0..1 subject 0..* participantRole typeCode*: <= ParticipationType contextControlCode*: CS CNE [1..1] <= "OP" time: IVL<TS> [0..1] awarenessCode: CE CWE [0..1] <= TargetAwareness participant 0..* assignedEntity performer typeCode*: <= PRF time: IVL<TS> [0..1] modeCode: CE CWE [0..1] <= ParticipationMode 0..1 assignedPerson 0..1 representedOrganization AssignedEntity 0..* observationRange typeCode*: <= REFV referenceRange ObservationRange classCode*: <= OBS moodCode*: <= EVN.CRT code: CD CWE [0..1] <= ActCode text: ED [0..1] value: ANY [0..1] interpretationCode: CE CNE [0..1] <= ObservationInterpretation Organizer classCode*: <= x_ActClassDocumentEntryOrganizer moodCode*: <= EVN id: SET<II> [0..*] code: CD CWE [0..1] <= ActCode statusCode*: CS CNE [1..1] <= ActStatus effectiveTime: IVL<TS> [0..1] The Organizer clone can be the source
  • f the component relationship or
the reference relationship, but not the entryRelationship relationship. Constraint: Organizer Act classCode*: <= x_ActClassDocumentEntryAct moodCode*: <= x_DocumentActMood id: SET<II> [0..*] code*: CD CWE [1..1] <= ActCode negationInd: BL [0..1] text: ED [0..1] statusCode: CS CNE [0..1] <= ActStatus effectiveTime: IVL<TS> [0..1] priorityCode: CE CWE [0..1] <= ActPriority languageCode: CS CNE [0..1] <= HumanLanguage 0..1 manufacturedProduct * typeCode*: <= PRD product Material classCode*: <= MMAT determinerCode*: <= KIND code: CE CWE [0..1] <= MaterialEntityClassType name: EN [0..1] lotNumberText: ST [0..1] LabeledDrug classCode*: <= MMAT determinerCode*: <= KIND code: CE CWE [0..1] <= DrugEntity name: EN [0..1] DrugOrOtherMaterial Organization classCode*: <= ORG determinerCode*: <= INSTANCE id: SET<II> [0..*] name: SET<ON> [0..*] telecom: SET<TEL> [0..*] addr: SET<AD> [0..*] standardIndustryClassCode: CE CWE [0..1] <= OrganizationIndustryClass 0..* specimenRole typeCode*: <= SPC specimen 0..1 specimenPlayingEntity SpecimenRole classCode*: <= SPEC id: SET<II> [0..*] Organization ParentDocument.text can be used to indicate the MIME type of the related document. It is not to be used to embed the related document, and thus ParentDocument.text.BIN is precluded from use. Constraint: ParentDocument.text ServiceEvent classCode*: <= ACT moodCode*: <= EVN id: SET<II> [0..*] code: CE CWE [0..1] effectiveTime: IVL<TS> [0..1] 0..* assignedEntity performer typeCode*: <= x_ServiceEventPerformer functionCode: CE CWE [0..1] <= ParticipationFunction time: IVL<TS> [0..1] 0..1 assignedPerson 0..1 representedOrganization AssignedEntity A conformant CDA document can have a single relatedDocument with typeCode "APND"; a single relatedDocument with typeCode "RPLC"; a single relatedDocument with typeCode "XFRM"; two relatedDocuments with typeCodes "XFRM" and "RPLC"; or two relatedDocuments with typeCodes "XFRM" and "APND". Constraint: relatedDocument.typeCode 0..1 wholeOrganization OrganizationPartOf 0..1 asOrganizationPartOf classCode*: <= PART id*: SET<II> [0..*] code: CE CWE [0..1] <= RoleCode statusCode: CS CNE [0..1] <= RoleStatus effectiveTime: IVL<TS> [0..1] Note: Observation.value has cardinality [0..*], which doesn't show up in the Visio representation. component 0..* clinicalStatement typeCode*: <= COMP contextConductionInd*: BL [1..1] "true" sequenceNumber: INT [0..1] seperatableInd: BL [0..1]
slide-6
SLIDE 6

Haifa Research Lab

6

Instance Generation

OWL Ontology Standard-based Instances (e.g., CDA)

Instance Generation Engine

Data Source

Mapping local Vocabularies

Template Model

Conform to the Template Model Representing constraints

Java API Adapter CTS

slide-7
SLIDE 7

Haifa Research Lab

INFOR NFORMATION ON & KNOWLE KNOWLEDGE GE

Genotype -> phenotype…

7

slide-8
SLIDE 8

Haifa Research Lab

8

Hypergenes Data Model

CDA Template

Header subject id …. Body

reference to PD

…. clinical & environmental

  • bservations

GV Template

subject id

Genomic Obs

Phenotype

Raw Genomic Data

subject id HapMap / BSML / MAGE Relational schemas

  • ptimized for persistency

Encapsulation

Pedigree Template

subject id

Disease Model

knowledge

Observed

EHR

  • r

GV Template

analysis id Analysis Workflow Run results

Genotype Phenotype

Interpretive

slide-9
SLIDE 9

Haifa Research Lab

9

HL7 Clinical Genomics Domain Information Model Adjusted to Knowledge Representation

0..* associatedObservation typeCode*: < ActRelationshipType (default=COMP) contextConductionInd: BL [0..1] "TRUE" sourceOf 0..* associatedProperty typeCode*: <= DRIV inversionInd: BL [1..1] ="TRUE" contextConductionInd: BL [0..1] "TRUE" derivedFrom 0..* sequenceVariation typeCode*: <= COMP contextConductionInd: BL [0..1] "TRUE" component1 Allele classCode*: <= SEQVAR moodCode*: <= DEF id: II [0..1] negationInd: BL [0..1] title: ED [0..1] text: ED [0..1] statusCode: CS CNE [0..1] < ActStatus effectiveTime*: GTS [1..1] activityTime: GTS [0..1] availabilityTime: TS [0..1] reasonCode: SET<CE> CWE [0..*] < ActReason value: ANY CWE [0..1] < ObservationValue GeneticLocus classCode*: <= LOC moodCode*: <= DEF id: II [0..1] code: CE CWE [0..1] < ActCode (default=Gene) negationInd: BL [0..1] title: ED [0..1] text: ED [0..1] statusCode: CS CNE [0..1] < ActStatus effectiveTime*: IVL<TS> [1..1] activityTime: GTS [0..1] availabilityTime: TS [0..1] confidentialityCode: SET<CE> CWE [0..*] < Confidentiality reasonCode: SET<CE> CWE [0..*] < ActReason value*: ANY CWE [1..1] < ObservationValue methodCode*: SET<CE> CWE [1..1] < ObservationMethod 0..* individualAllele typeCode*: <= COMP contextConductionInd: BL [0..1] "TRUE" component1 Sequence classCode*: <= SEQ moodCode*: <= DEF id: II [0..1] code: CD CWE [1..1] < ActCode (the type of sequence (OBSERVED, REFERENCE, etc.) text: ED [0..1] (sequence's annotations) effectiveTime: GTS [0..1] activityTime: GTS [0..1] availabilityTime: TS [0..1] reasonCode: SET<CE> CWE [0..*] < ActReason value: ED [1..1] ((the actual sequence in a recognized bioinformatics content model) (such as BSML) methodCode: SET<CE> CWE [0..*] < ObservationMethod (the sequencing method) Note: A related allele that is at a different locus, and has interrelation with the source allele, e.g., translocated duplicates
  • f a gene.
0..* phenotype typeCode*: <= PERT contextConductionInd: BL [0..1] "TRUE" uncertaintyCode: CE CNE [0..1] < ActUncertainty pertinentInformation SequenceVariation classCode*: <= SEQVAR moodCode*: <= DEF id: II [0..1] code: CD CWE [0..1] < ActCode negationInd: BL [0..1] title: ED [0..1] text: ED [0..1] effectiveTime: GTS [0..1] activityTime: GTS [0..1] availabilityTime: TS [0..1] value: ANY CWE [0..1] < ObservationValue methodCode: SET<CE> CWE [0..*] < ObservationMethod Note: Code: COPY_NUMBER, ZYGOSITY, DOMINANCY, GENE_FAMILY,
  • etc. For example, if code = COPY_NUMBER, then the value is of
type INT and is holding the no. of copies of this gene or allele. 0..* sequence typeCode*: <= COMP component3 0..* phenotype typeCode*: <= PERT contextConductionInd: BL [0..1] "TRUE" uncertaintyCode: CE CNE [0..1] < ActUncertainty pertinentInformation 0..* phenotype typeCode*: <= PERT contextConductionInd: BL [0..1] "TRUE" uncertaintyCode: CE CNE [0..1] < ActUncertainty pertinentInformation Note: Use the associations to the shadow classes when the variation and or the sequence data are not at the allelic level. 0..* associatedObservation typeCode*: < ActRelationshipType (default=COMP) contextConductionInd: BL [0..1] "TRUE" sourceOf 0..1 associatedObservation typeCode*: < ActRelationshipType (default=COMP) contextConductionInd: BL [0..1] "TRUE" sourceOf Note: This recursive association enables the association of an RNA sequence derived from a DNA sequence and a polypeptide sequence derived from the RNA sequence. 0..* phenotype typeCode*: <= PERT contextConductionInd: BL [0..1] "TRUE" uncertaintyCode: CE CNE [0..1] < ActUncertainty pertinentInformation Note: This class is a placeholder for specifying a locus on the genome, i.e., a position of a particular given sequence in the genome. Note that the semantics of the locus (e.g., gene, biomarker, etc.) is defined by data assigned in the code & value attributes of this class, and also by placing additional data relating to this locus into the classes (and CMETs) associated with this class. AssociatedObservation classCode*: <= GEN moodCode*: <= DEF (default=EVN) id: SET<II> [0..*] code*: CD CWE [1..1] <= ActCode text: ED [0..1] effectiveTime*: GTS [1..1] activityTime: GTS [0..1] availabilityTime: TS [0..1] value: ANY CWE [0..1] <= ObservationValue methodCode: SET<CE> CWE [0..*] <= ObservationMethod Note: The code attribute could hold codes like TYPE, POSITION.GENOME, LENGTH, REFERENCE, REGION, etc.. The value attribute is populated based on the selected code and its data type is then setup accordingly during instance
  • creation. Here are a few examples:
If code = "DNA marker type" (LOINC code 48019-4), then the value (typed CE) holds one of the following codes, e.g., drawn from the respective LOINC value set: Wild type (LA9658-1), Deletion (LA6692-3), Duplication (LA6686-5), Insertion (LA6687-3), Insertion/Deletion (LA6688-1), Inversion (LA6689-9), Substitution (LA6690-7). if code = POSITION, then value is of type INT and holds the actual numeric value representing the variation position along the gene. if code = LENGTH, then value is of type INT and holds the actual numeric value representing the variation length. If the code = REFERENCE, then value is type CD and holds the reference gene identifier drawn from a reference database like GenBank. More details about vocabularies for codes and its respective values could be found in the specification. Note: Code: CLASSIFICATION, etc. For example, if code = CLASSIFICATION, then the value is of type CV and is holding either KNOWN or NOVEL. reference 0..* geneticLocus typeCode*: <= REFR contextConductionInd: BL [0..1] "FALSE" Note: A related locus that has significant interrelation with the source locus and is not part of this loci set represented in this instance. For example, the target could be a presumed locus that is associated with this locus representing a genetic marker. reference 0..* individualAllele typeCode*: <= REFR contextConductionInd: BL [0..1] "TRUE" Constrained to a restricted BSML content model, specified in a separate schema. Constraint: Sequence.value 0..* sequence typeCode*: <= COMP contextConductionInd: BL [0..1] "TRUE" component3 0..* sequenceVariation typeCode*: <= COMP contextConductionInd: BL [0..1] "TRUE" component2 AssociatedProperty classCode*: <= GEN moodCode*: <= DEF (default=EVN) code*: CD CWE [1..1] <= ActCode text: ED [0..1] value: ANY CWE [0..1] <= ObservationValue 0..* associatedProperty typeCode*: <= DRIV inversionInd: BL [1..1] ="TRUE" contextConductionInd: BL [0..1] "TRUE" derivedFrom 0..* associatedProperty typeCode*: <= DRIV inversionInd: BL [1..1] ="TRUE" contextConductionInd: BL [0..1] "TRUE" derivedFrom 0..* associatedProperty typeCode*: <= DRIV contextConductionInd: BL [0..1] "TRUE" derivedFrom1 0..* associatedObservation typeCode*: < ActRelationshipType (default=COMP) contextConductionInd: BL [0..1] "TRUE" sourceOf 0..* sequenceVariation typeCode*: <= DRIV inversionInd: BL [0..1] ="TRUE" contextConductionInd: BL [0..1] "TRUE" derivedFrom4 derivedFrom2 0..* sequence typeCode*: <= DRIV inversionInd: BL [0..1] ="TRUE" contextConductionInd: BL [0..1] "TRUE" Note: Any observation related to the variation and is not an inherent part of the variation observation (the latter should be represented in the AssociatedProperty class). For example, the zygosity of the variation. Note: Any observation related to the sequence and is not an inherent part of the sequence observation, e.g., splicing alternatives. Note that inherent characteristics of the sequence should be represented in the AssociatedProperty class. Note: There could be zero to many IndividualAllele objects in a specific instance. A typical case would be an allele pair,
  • ne on the paternal
chromosome and one on the maternal chromosome. Note: Use this class for inherent data about the locus, e.g. chromosome no. 0..* phenotype typeCode*: <= PERT pertinentInformation AssociatedProperty AssociatedProperty AssociatedProperty SequenceVariation Sequence SequenceVariation Note: An internal CMET used to represent clinical phenotypes, both observed in the patient and known in the scientific literature. Holds the variation expressed with a recognized notation like 269T>C or a markup like BSML or drawn from an external reference like OMIM or dbSNP. Data type should be set accordingly. Constraint: value If code = "Gene", value data type shall be set to CD and contain a code identifying a gene through GenBank GeneID, HUGO name, OMIM ID or any other internationally recognized identification of genes. If the locus is not a gene then the data type should be set to the appropriate type, e.g., ST for locus notation like “10q24.32”. Constraint: value GeneticLoci classCode*: <= LOC moodCode*: <= DEF id: II [0..1] code*: CD CWE [1..1] <= GeneticVariation negationInd: BL [0..1] title: ED [0..1] text: ED [0..1] statusCode*: CS CNE [1..1] < ActStatus effectiveTime*: GTS [1..1] activityTime: GTS [0..1] availabilityTime: TS [0..1] confidentialityCode: SET<CE> CWE [1..1] < Confidentiality reasonCode: SET<CE> CWE [0..*] < ActReason value: ANY CWE [0..1] < ObservationValue methodCode: SET<CE> CWE [0..*] < ObservationMethod 0..* geneticLocus typeCode*: <= COMP component1 0..* assignedEntity typeCode*: <= AUT contextControlCode: CS CNE [0..1] "OP" author CMET: (ASSIGNED) R_AssignedEntity [universal] (COCT_MT090000UV) 0..1 roleName 0..* associatedObservation typeCode*: < ActRelationshipType (default=COMP) contextConductionInd: BL [0..1] "TRUE" sourceOf 0..* phenotype typeCode*: <= PERT contextConductionInd: BL [0..1] "TRUE" uncertaintyCode: CE CNE [0..1] < ActUncertainty pertinentInformation AssociatedObservation AssociatedObservation AssociatedObservation AssociatedObservation If interpretationCode is assigned with a value a reasonCode shall be assigned a value to set the context for the interpretation semantics. Constraint: GeneticLoci.reasonCode&interpretationCode 0..* associatedProperty typeCode*: <= DRIV inversionInd: BL [1..1] ="TRUE" contextConductionInd: BL [0..1] ="TRUE" derivedFrom Note: Use the value attribute to encapsulate raw data relating to the entire set of loci. For example, SNP genotyping of a large number of genes/markers. Note: The attribute inversionInd is fixed to “TRUE” to indicate that the associated property is derived from the source class and not vice versa. CMET: (PHN) A_Phenotype [universal] (COCT_MT340000UV) CMET: (PHN) A_Phenotype [universal] (COCT_MT340000UV) CMET: (PHN) A_Phenotype [universal] (COCT_MT340000UV) CMET: (PHN) A_Phenotype [universal] (COCT_MT340000UV) CMET: (PHN) A_Phenotype [universal] (COCT_MT340000UV) CMET: (PHN) A_Phenotype [universal] (COCT_MT340000UV) component2 0..* geneticLoci typeCode*: <= COMP The code attribute indicates the type
  • f representation used in the value
attribute, e.g., dbSNP, HGVS, BSML. Constraint: code CMET: (ACT) A_Annotation [universal] (COCT_MT590000UV) 0..* annotation typeCode*: <= SUBJ contextControlCode: CS CNE [0..1] ="AN" contextConductionInd: BL [0..1] ="false" sequenceNumber: INT [0..1] seperatableInd: BL [0..1] ="false" subject HL7 Clinical Genomics SIG Document: Clinical Genomics DIM Rev: POCG_DM000020.v5 Date: Jull 22, 2009 Facilitator: Amnon Shabo (Shvo), IBM Research in Haifa, shabo@il.ibm.com Genome classCode*: <= GEN moodCode*: <= DEF id: SET<II> [0..*] code: CD CWE [0..1] <= ActCode text: ED [0..1] effectiveTime: GTS [0..1] activityTime: GTS [0..1] availabilityTime: TS [0..1] confidentialityCode: SET<CE> CWE [0..*] <= Confidentiality value: ANY CWE [0..1] <= ObservationValue methodCode: SET<CE> CWE [0..*] <= ObservationMethod 0..* geneticLoci typeCode*: <= COMP component1 LargeDeletion classCode*: <= GEN moodCode*: <= EVN id: SET<II> [0..*] code: CD CWE [0..1] < ActCode text: ED [0..1] effectiveTime: GTS [0..1] activityTime: GTS [0..1] availabilityTime: TS [0..1] confidentialityCode: SET<CE> CWE [0..*] < Confidentiality uncertaintyCode: CE CNE [0..1] < ActUncertainty value: ANY CWE [0..1] < ObservationValue methodCode: SET<CE> CWE [0..*] < ObservationMethod 0..* nonLocusData typeCode*: <= COMP contextControlCode: CS CNE [0..1] < ContextControlPropagating contextConductionInd: BL [0..1] "true" component2 Cytogenetics classCode*: <= GEN moodCode*: <= EVN id: SET<II> [0..*] code: CD CWE [0..1] < ActCode text: ED [0..1] effectiveTime: GTS [0..1] activityTime: GTS [0..1] availabilityTime: TS [0..1] confidentialityCode: SET<CE> CWE [0..*] < Confidentiality uncertaintyCode: CE CNE [0..1] < ActUncertainty value: ANY CWE [0..1] < ObservationValue methodCode: SET<CE> CWE [0..*] < ObservationMethod OtherNonLocusData classCode*: <= GEN moodCode*: <= EVN id: SET<II> [0..*] code: CD CWE [0..1] < ActCode text: ED [0..1] effectiveTime: GTS [0..1] activityTime: GTS [0..1] availabilityTime: TS [0..1] confidentialityCode: SET<CE> CWE [0..*] < Confidentiality uncertaintyCode: CE CNE [0..1] < ActUncertainty value: ANY CWE [0..1] < ObservationValue methodCode: SET<CE> CWE [0..*] < ObservationMethod LargeDuplication classCode*: <= GEN moodCode*: <= EVN text: ED [0..1] effectiveTime: GTS [0..1] activityTime: GTS [0..1] availabilityTime: TS [0..1] confidentialityCode: SET<CE> CWE [0..*] < Confidentiality uncertaintyCode: CE CNE [0..1] < ActUncertainty value: ANY CWE [0..1] < ObservationValue methodCode: SET<CE> CWE [0..*] < ObservationMethod Clinical Genomics DIM (POCG_DM000020UV) A derivative of the Domain Information Model, to make it capable of representing knowledge that is not tied to to a specific subject. 0..* expression typeCode*: <= COMP component2 GeneticLoci (POCG_RM000055UV) The entry point to the GeneticLoci (and the constrained GeneticVariation) model. Polypeptide classCode*: <= POL moodCode*: <= DEF id: II [0..1] text: ED [0..1] effectiveTime: GTS [0..1] value: CD CWE [0..1] <= ObservationValue (protein code, drawn from SwissProt, PDB, PIR, HUPO, etc.) methodCode: SET<CE> CWE [0..*] <= ObservationMethod DeterminantPeptide classCode*: <= DETPOL moodCode*: <= DEF id: II [0..1] text: ED [0..1] effectiveTime: GTS [0..1] value: CD CWE [0..1] < ObservationValue ((((((((peptide code, drawn from reference databases like)) ((those)))) ((((used) (in) (the Polypeptide class) methodCode: SET<CE> CWE [0..*] < ObservationMethod Note: This is a computed outcome, i.e., the lab does not test for the actual protein, but secondary processes populate this class with the translational protein. 0..* determinantPeptide typeCode*: <= DRIV derivedFrom1 0..* phenotype typeCode*: <= PERT pertinentInformation 0..* phenotype typeCode*: <= PERT pertinentInformation Note: Key peptides in the protein that determine its function. Note: The code attribute holds codes that identify the types of property held in the value attribute. 0..* associatedObservation typeCode*: <= COMP component 0..* associatedProperty typeCode*: <= DRIV derivedFrom2 0..* polypeptide typeCode*: <= DRIV derivedFrom3 Expression classCode*: <= EXP moodCode*: <= DEF id: II [0..1] code: CE CWE [1..1] <= ActCode (the standard's code (e.g., MAGE-ML identifier) negationInd: BL [0..1] text: ED [0..1] effectiveTime: GTS [0..1] activityTime: GTS [0..1] availabilityTime: TS [0..1] uncertaintyCode: CE CNE [0..1] <= Uncertainty value: ED [1..1] (the actual gene or protein expression levels) methodCode: SET<CE> CWE [0..*] <= ObservationMethod 0..* phenotype typeCode*: <= PERT pertinentInformation Note: The Expression class refers to both gene and protein expression
  • levels. It is an encapsulating class
that allows the encapsulation of raw expression data in its value attribute. Note: The code attribute could hold codes like NORMALIZED_INTENSITY, P_VALUE, etc. The value attribute is populated based on the selected code and its data type is then setup accordingly during instance creation. 0..* associatedObservation typeCode*: <= COMP component 0..* associatedProperty typeCode*: <= DRIV derivedFrom Note: Any observation related to the expression assay and is not an inherent part of the expression
  • bservation.
Constrained to a restricted MAGE-ML content model, specified in a separate schema. Constraint: Expression.value Expression (POCG_RM000031UV) Entry point to the Expression data internal CMET used by the Clinical Genomics models. CMET: (PHN) A_Phenotype [universal] (COCT_MT340000UV) CMET: (PHN) A_Phenotype [universal] (COCT_MT340000UV) AssociatedProperty AssociatedObservation AssociatedObservation AssociatedProperty AssociatedProperty 0..* author1 NonLocusData Expression 0..* expression typeCode*: <= COMP component4 Expression 0..* expression typeCode*: <= COMP component3 component 0..* associatedObservation typeCode*: <= COMP 0..* phenotype typeCode*: <= PERT pertinentInformation CMET: (ACT) A_Phenotype [universal] (COCT_MT340000UV) 0..* associatedProperty typeCode*: <= DRIV inversionInd: BL [1..1] ="TRUE" contextConductionInd: BL [0..1] ="TRUE" derivedFrom AssociatedProperty 0..1 associatedObservation typeCode*: < ActRelationshipType (default=COMP) contextConductionInd: BL [0..1] "TRUE" sourceOf AssociatedObservation derivedFrom 0..* associatedObservation typeCode*: <= DRIV CMET: (ACT) A_Phenotype [universal] (COCT_MT340000UV) 0..* phenotype typeCode*: <= PERT pertinentInformation

Genome Genetic Loci Genetic Locus Sequence Non- locus specific data Peptide Expression Sequence Variation Allele Phenotype

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Analysis Knowledge GV Template § Analysis meta information

§ Analysis title and unique identifier § Analysis type § Performer details: name, organization, OID…

§ Analysis workflow

§ IBM Bio-clinical Data Mining (BDM) tool on AlphaWorks, http://www.alphaworks.ibm.com/tech/bdm

§ Analysis results

§ Effective time of analysis results § Risk Allele § SNP – Gene id, chromosomal coordinate § Risk allele pvalue § Non risk counterpart allele § Associated phenotype

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Haifa Research Lab

Subject Specific GV Knowledge Template § Metadata

§ Effective creation time § Unique instance identifier

§ Subject details

§ Identification / Organization

§ Subject SNPs

§ Genotyping center / device § SNP alleles from genomic data § Only intersection of SNPs relevant for analysis are taken

§ Subject Clinical data

§ HL7 references to observations from clinical records (CDAs)

§ Analyses results impact on subject

§ Analysis id / reference to CG instance § Risk alleles for subject

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Haifa Research Lab

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Thank You J J

The End