Bridging Epoch: Mapping Two Clinical Trial Ontologies · Bridging Epoch: Mapping Two Clinical Trial...
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Bridging Epoch: Mapping Two Clinical Trial Ontologies
10th International Protégé ConferenceJuly 17, 2007
Samson W. Tu1, Douglas Fridsma2, Ravi D. Shankar1, Martin O'Connor1, Amar K. Das1, David B. Parrish3
1Stanford University, USA2University of Pittsburgh, USA
3The Immune Tolerance Network, Pittsburgh, PA, USA
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Problem: Ontologies and semantic interoperability
Ontology 1Ontology 2
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BRIDG: Biomedical Research Integration Group
Part of US NCI Cancer Biomedical Informatics Grid (caBIG)Stakeholders include US FDA, HL7, CDISCCreate shared domain model for protocol-driven clinical research
ComprehensiveConsensus-basedAbstract and context neutral
BRIDG
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EPOCH: Immune Tolerance Network clinical trial ontologies
Immune Tolerance Network (ITN)International collaborative research effort that sponsors clinical trials and mechanistic assays on immune tolerance
EPOCH clinical trial modelDeveloped at Stanford Medical InformaticsDesigned to provide semantic foundation for management of clinical trials
EPOCH
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Management of clinical trials involves complex data and multiple groups
ProtocolGroup
Schedule of Events
CRO
CRF
Data Center
AccessionAccessionIDCoreID (FK)FilenameTransmissionDtTransactionCodeID (FK)RecordDtUserID (FK)
ArchiveArchiveIDCoreID (FK)ProcessID (FK)NameDirectoryRecordDtUserID (FK)
BarcodeBarcodeIDStudyID (FK)SubjectID (FK)VisitID (FK)BarcodeCollectionDtRecordDtUserID (FK)
ConfigParameterConfigParameterIDProcessID (FK)NameValueRecordDtUserID (FK)
DescriptionRecordDtUserID (FK)
Core_AssaysCoreID (FK)AssayID (FK)SpecimenTypeID (FK)RecordDtUserID (FK)
Core_ContactsCoreID (FK)ContactTypeID (FK)UserID (FK)RecordDt
Core_Issues
IssueIDCoreStudyCoresampleIDRequestedByDescriptionRequestDtResponseStatusCoreSampleID (FK)
CoreSample
CoreSampleIDStudyID (FK)AccessionID (FK)ProcessingCodeID (FK)SampleTypeID (FK)RecdDtAnalysisDtTechnameFilenameExternalIDBarcodeID9SpecimenTypeID (FK)RecordDtUserID (FK)
CoreSample_Detail
CoreSampleID (FK)BarcodeID (FK)QCSampleID (FK)ValidationCodeID (FK)ValidationDtRecordDtUserID (FK)
CoreSample_DevCodeCoreSampleID (FK)DevCodeID (FK)NotesRecordDtUserID (FK)
DevCodeDevCodeID
CodeDescriptionGetCommentsRecordDtUserID (FK)
ampleID (FK)D (FK)D(FK)FK)D(FK)(FK)meeID (FK)ntdDtD(FK)
FieldFieldIDNameDescriptionRecordDtUserID (FK)
FileRequestRequestIDRequestDtCompletedDtEmailAddressStatusFileNameFileTypeMessageArchiveID (FK)UserName
FileRequestList
FileRequestListIDStatusFileNameDirectoryRequestID (FK)Message
K)
pcrResult_Qual
CoreSampleid (FK)TestID (FK)ReplicateIDBaseVisitID (FK)QualifierAtLeastSampleQualityCalibratorQualityRecordDtUserID (FK)
ProcessProcessIDNameRecordDtUserID (FK)
ProcessingCodeProcessingCodeIDCodeDescriptionRecordDtUserID (FK)
SMS_Acc
Study_IDSite_IDParticipanVisit_NumCollectionCollectionBarcodeSpecimenLabSite_Dev_Core_DevO_Study_O_Site_IDO_ParticiO_Visit_NO_CollecO_CollecO_SpecimInvalidStaInvalidCoInvalidCoInvalidSIDInvalidPIDInvalidEnRecordDt
SMS_Issued_QueriesIssueID (FK)Query_ID (FK)RecordDtResolved
SMS_IssuesIssueIdCoreSampleID (FK)TextMsgStatusRecordDt
SMS_Qu
QueryStudyQuerySite_qQueryQueryQueryQueryDate_Date_Date_InitiatResolExternResolDate_Query
SourceSourceID
CoreID (FK)VersionDescriptionStartDtEndDtRecordDtUserID (FK)
Source_FieldsSourceFieldID
SourceID (FK)FieldID (FK)OrdinalRecordDtSkipFlagRecordDtUserID (FK)
SampleTypeSampleTypeIDNameRecordDtUserID (FK)
CodeConvNumIsLocalLabIRBApprovedlDtITNApprovedDtBudgetApprovedDtActivationDtRecordDtUserID (FK)
SubjectSubjectIDSiteID (FK)ParticipantIDStudyGroupID (FK)RecordDtUserID (FK)
TransactionCode
TransactionCodeIDCodeDescriptionRecordDtUserID (FK)
ValidationCodeValidationCodeIDCodeDescriptionRecordDtUserID (FK)
rptDataExtractRequestRequestNumberDtOfRequestDtRequiredByRequestorNameRequestorPhoneStudyNumCoreStudyDataQCSamplesResearchDevelopmentStartDtEndDtVisitsDetailDataFormatIncludeDeviationCodesIncludeTrtCohortIncludeUnvalidatedSamplesSpecialInstructionsAssignedToAssignedDtPlanStatusDtPlanAvailableDtPlanFinalRequestClosedByClosedDtSiteDetailsInformaticsNoteRecUpdatedByRecUpdatedOnDataExtractType
D(FK)reID (FK)FK)
Dt(FK)
Scee g tEnrollmentDtStudyGroupID (FK)DonorIDRecipientIDRecordDtScreeningFailureResasonIDScreeningFailureCommentUserID (FK)
ETLMappingDetailMapDtlIDSourceColumnTargetTableTargetColumnTypeMapHdrID
ETLMappingHeaderMapHdrIDMappingNameSourceVersion
GenericLoadGenLoadIDFileNameFileDirRowNumberColumnNameCellValueSourceVersiondtEnteredLoadID
GenericLoadBatchGLBatchID
FileDirRecordDtFileName
HLABusinessRuleDetailBRDetailIDTargetTableTargetColumnBRValueTargetColumnTypeBRHdrID
HLABusinessRuleHeaderBRHdrIDVersionBRName
HLADataImportLogImportLogIDFileNameStudyNumCodeVisitNumSpecimenTypeParticipantIDBarcodeDescriptionRecordDtOperatorIDAccessionID
HLAEvertLogHLAEventLogIDEventDescRecordDtOperatorIDGLBatchID
ScreeningFailureReasonScreeningFailureReasonIDCodeDescriptionEnabledStudyID
TransplantTransplantIdRecipient_SubjectIdDonor_SubjectIdOrganRecordDtOperatorStudyId
Clinical Trial Data
Cimarron
ImmunoTrak
CoreLabs
AssayResults
Tubes Manufacturer
KitReport
Assay Group
OperationsGroup
SpecimenTable
TubeTable
QueriesReports
QueriesReports
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Three goals of EPOCHontologies
Design tools to help acquire and maintain knowledge about protocol and assay designsUse this knowledge to drive data collectionduring a trialImplement querying methods to support trial management, and ad hoc data analysis
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EPOCH ontologies created in Protégé OWL
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ITN wants to use BRIDG-compliant applications
ITN protocols encoded as EPOCHknowledge bases to drive caBIG applications (e.g., Patient Study Calendar)Challenge: Develop methods to
Harmonize common subset of BRIDG & EPOCH: shared semanticsOvercome representational mismatch
• Representation languages• Representation choices• (Terminological mismatch not consider here)
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Approach taken
Semantic alignmentOvercoming representation language mismatch Overcoming representation choice mismatches
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Approach taken
Semantic alignmentUse Excel spreadsheet to systematically review and document possible mappingsDefine necessary preconditions for mapping
Overcoming representation language mismatch Overcoming representation choice mismatches
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Semantic Alignment: Excel spreadsheet
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Semantic Alignment: Restrictions on EPOCH
Mapping from EPOCH to BRDG => Place restrictions on EPOCH
Only one schedule of activitiesPeriod has no subperiodsLimited temporal annotations…
Define necessary conditions for mappingFormulate as DL definition of “BRIDGClinicalTrial” subclass of epoch:ClinicalTrial
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BRIDGClinicalTrial in EPOCH
Need trial-specific closure axioms to do automated classification of EPOCH trials that can be mapped to BRIDG
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Approach taken
Semantic alignmentOvercoming representation language mismatch Overcoming representation choice mismatches
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Overcoming representation language mismatch: BRIDG-in-OWL
Scope: BRIDG Study Planned View + BRIDG Complex Data Types
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Example: PlannedStudy
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Modifications to BRIDG
Driven by Patient Study Calendar application requirementsAdded several associational relationshipsModified some subsumption relations
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Approach taken
Semantic alignmentOvercoming representation language mismatch Overcoming representation choice mismatches
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Overcoming representation choice mismatch: Epoch example
Period
Screening0
Arm1Cycle1 Arm1Cycle2
PeriodType=Screening
PeriodType=Intervention PeriodType=Intervention
Arm2Cycle1 Arm2Cycle2PeriodType=Intervention PeriodType=Intervention
Intervention epochScreening epoch
EPOCH
BRIDG
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SWRL rule to map epochs
EPOCH:periodTypes of periods correspond to BRIDG:epochsEPOCH :periodType.label corresponds toBRIDG:epoch.code.displayName
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Successfully used an EPOCH clinical trial to configure BRIDG Patient Study Calendar application
Herold protocolin EPOCH
Herold protocolin BRIDG
Herold protocolin PSC XML
SWRL rules SWRL rules Patient StudyCalendar
Automated mappings except for onerelationship
Because of OWL/SWRL’s open-world assumption, First epoch cannot be derived as an epoch that has no predecessor
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Conclusions
Semantic interoperability requiresHarmonization of subsets of ontologies/modelsOvercoming mismatches in representation languages and representation choices
OWL restrictions and SWRL rules help toovercome semantic and syntactic mismatchesPossible future work
Continued harmonization of BRIDG/EPOCHScalability and (semi-)automation of method
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Thank you!
Questions?Comments?Suggestions?