Epoch Ontological Framework to support Clinical … Ontological Framework to support Clinical Trial...
Transcript of Epoch Ontological Framework to support Clinical … Ontological Framework to support Clinical Trial...
Epoch Ontological Framework to support Clinical Trial Management
Ravi ShankarStanford Medical Informatics
Stanford University
Overview
Clinical trials are used to determine whether new drugs or treatments are both safe and effective.
Complex clinical trials involve collaboration among many groups using different software applications.
Lack of standardization and reduced efficiency leads to poor productivity.
We are building an ontological framework called Epoch to improve semantic interoperability among clinical trial management applications.
The Immune Tolerance Network
ITN is an international collaboration designed to accelerate the development of immune tolerance therapiesFunds, plans, implements, monitors, and assessesinvestigator-initiated clinical trials of novel tolerance-promoting therapies in
• Autoimmune diseases• Transplantation• Allergy and Asthma
Provides services to undertake comprehensive mechanistic studies that complement each trial
Schedule of Events
Schedule of Events
Visit
Period
TimeAnchor
Annotation
TemporalConstraint
Activity
Specimen Table
Specimen Table
Assay
ProcessingInstruction
MechanisticStudy
Specimen Workflow
Specimen Container
Specimen Workflow
RT PCRCore
KidneyCore
1 x cryovial(kidney)
1 x cryomold(kidney)
1 x cryovial(kidney)
–E21
1 x 0.5ml cryovial(kidney RNA)
1 x 0.5 cryovial(kidney RNA)
1 x cryomold(kidney)
Barcode Suffix – E22
FisherLab
RNA ProcessingCore
SpecimenDisposalPoint
1 x cryovial(kidney)
1 x cryomold(kidney)
1 x cryovial(kidney)
Barcode Suffix –E21
1 x 0.5ml cryovial(kidney RNA)
1 x 0.5 cryovial(kidney RNA)
1 x cryomold(kidney)
Barcode Suffix – E22
SpecimenCollectionPoint
RT PCRCore
KidneyCore
1 x cryovial(kidney)
1 x cryomold(kidney)
1 x cryovial(kidney)
–E21
1 x 0.5ml cryovial(kidney RNA)
1 x 0.5 cryovial(kidney RNA)
1 x cryomold(kidney)
Barcode Suffix – E22
FisherLab
RNA ProcessingCore
SpecimenDisposalPoint
1 x cryovial(kidney)
1 x cryomold(kidney)
1 x cryovial(kidney)
Barcode Suffix –E21
1 x 0.5ml cryovial(kidney RNA)
1 x 0.5 cryovial(kidney RNA)
1 x cryomold(kidney)
Barcode Suffix – E22
SiteLab
Core lab
Bio-RepositorySpecimen
Container
Specimen Workflow
SpecimenCollectionPoint
Challenges in Trials Management
Knowledge about protocols, assays, and specimen flow is captured in documents and spreadsheets
Plan Implement Monitor Assess
CoreCRF
Tracking
What is in a visit name?Visit 0, v0, v 0, 0, Day 0, Transplant
What is in a visit name?Visit 0, v0, v 0, 0, Day 0, Transplant
ProtocolGroup
Assay Group
0
0
Schedule of Events
SpecimenTable
What is in a visit name?Visit 0, v0, v 0, 0, Day 0, Transplant
ProtocolGroup
Assay Group
CRO Day 0, Transplant
0
0
CRF
Schedule of Events
SpecimenTable
What is in a visit name?Visit 0, v0, v 0, 0, Day 0, Transplant
ProtocolGroup
Assay Group
OperationsGroup
CRO
v 0
0
0
Day 0, Transplant
TubeTable
CRF
Schedule of Events
SpecimenTable
What is in a visit name?Visit 0, v0, v 0, 0, Day 0, Transplant
ProtocolGroup
Assay Group
OperationsGroup
CRO
Cimarron
Fisher
KitReport
Day 0, Transplant
0
0
v 0
v 0v0, Visit 0
ImmunoTrak
CRF
TubeTable
Schedule of Events
SpecimenTable
What is in a visit name?Visit 0, v0, v 0, 0, Day 0, Transplant
ProtocolGroup
Assay Group
OperationsGroup
Fisher
CoreLabs
CRO
Cimarron
0
0
Day 0, Transplant
v0
v0, Visit 0
v 0
v 0
KitReport
ImmunoTrak
Assays
CRF
TubeTable
Schedule of Events
SpecimenTable
What is in a visit name?Visit 0, v0, v 0, 0, Day 0, Transplant
CRO
ProtocolGroup
Assay Group
CimarronOperationsGroup
Data Center
CoreLabs
Fisher
Day 0, Transplant
v0
0
0
v 0
v 0v0, Visit 0
AccessionAccessionIDCoreID (FK)FilenameTransmissionDtTransactionCodeID (FK)RecordDtUserID (FK)
ArchiveArchiveID
CoreID (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_DetailCoreSampleID (FK)BarcodeID (FK)QCSampleID (FK)ValidationCodeID (FK)ValidationDtRecordDtUserID (FK)
CoreSample_DevCodeCoreSampleID (FK)DevCodeID (FK)NotesRecordDtUserID (FK)
DevCodeDevCodeID
CodeDescriptionGetCommentsRecordDtUserID (FK)
mpleID (FK)D (FK)D(FK)FK)D(FK)(FK)meeID (FK)tDt(FK)
FieldFieldIDNameDescriptionRecordDtUserID (FK)
FileRequestRequestIDRequestDtCompletedDtEmailAddressStatusFileNameFileTypeMessageArchiveID (FK)UserName
FileRequestList
FileRequestListIDStatusFileNameDirectoryRequestID (FK)Message
pcrResult_Qual
CoreSampleid (FK)TestID (FK)ReplicateIDBaseVisitID (FK)QualifierAtLeastSampleQualityCalibratorQualityRecordDtUserID (FK)
Process
ProcessIDNameRecordDtUserID (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)
rptDataExtractRequestRequestNumber
DtOfRequestDtRequiredByRequestorNameRequestorPhoneStudyNumCoreStudyDataQCSamplesResearchDevelopmentStartDtEndDtVisitsDetailDataFormatIncludeDeviationCodesIncludeTrtCohortIncludeUnvalidatedSamplesSpecialInstructionsAssignedToAssignedDtPlanStatusDtPlanAvailableDtPlanFinalRequestClosedByClosedDtSiteDetailsInformaticsNoteRecUpdatedByRecUpdatedOnDataExtractType
(FK)reID (FK)FK)
Dt(FK)
Sc ee g tEnrollmentDtStudyGroupID (FK)DonorIDRecipientIDRecordDtScreeningFailureResasonIDScreeningFailureCommentUserID (FK)
ETLMappingDetailMapDtlIDSourceColumnTargetTableTargetColumnTypeMapHdrID
ETLMappingHeaderMapHdrIDMappingNameSourceVersion
GenericLoadGenLoadIDFileNameFileDirRowNumberColumnNameCellValueSourceVersiondtEnteredLoadID
GenericLoadBatchGLBatchID
FileDirRecordDtFileName
HLABusinessRuleDetailBRDetailIDTargetTableTargetColumnBRValueTargetColumnTypeBRHdrID
HLABusinessRuleHeaderBRHdrIDVersionBRName
HLADataImportLogImportLogID
FileNameStudyNumCodeVisitNumSpecimenTypeParticipantIDBarcodeDescriptionRecordDtOperatorIDAccessionID
HLAEvertLogHLAEventLogIDEventDescRecordDtOperatorIDGLBatchID
ScreeningFailureReasonScreeningFailureReasonIDCodeDescriptionEnabledStudyID
TransplantTransplantIdRecipient_SubjectIdDonor_SubjectIdOrganRecordDtOperatorStudyId
DatabaseKit
Report
ImmunoTrak
Assays
CRF
TubeTable
Schedule of Events
SpecimenTable
ITN_BioMed V5Schema
AccessionAccessionIDCoreID (FK)FilenameTransmissionDtTransactionCodeID (FK)RecordDtUserID (FK)
ArchiveArchiveIDCoreID (FK)ProcessID (FK)NameDirectoryRecordDtUserID (FK)
BarcodeBarcodeIDStudyID (FK)SubjectID (FK)VisitID (FK)BarcodeCollectionDtRecordDtUserID (FK)
ConfigParameterConfigParameterIDProcessID (FK)NameValueRecordDtUserID (FK)
ContactTypeContactTypeIDNameRecordDtUserID (FK)
Core
CoreIDLocationID (FK)CodeDescriptionRecordDtUserID (FK)
Core_AssaysCoreID (FK)AssayID (FK)SpecimenTypeID (FK)RecordDtUserID (FK)
Core_ContactsCoreID (FK)ContactTypeID (FK)UserID (FK)RecordDt
Core_IssuesIssueIDCoreStudyCoresampleIDRequestedByDescriptionRequestDtResponseStatusCoreSampleID (FK)
CoreSampleCoreSampleIDStudyID (FK)AccessionID (FK)ProcessingCodeID (FK)SampleTypeID (FK)RecdDtAnalysisDtTechnameFilenameExternalIDBarcodeID9SpecimenTypeID (FK)RecordDtUserID (FK)
CoreSample_DetailCoreSampleID (FK)BarcodeID (FK)QCSampleID (FK)ValidationCodeID (FK)ValidationDtRecordDtUserID (FK)
CoreSample_DevCodeCoreSampleID (FK)DevCodeID (FK)NotesRecordDtUserID (FK)
DevCodeDevCodeID
CodeDescriptionGetCommentsRecordDtUserID (FK)
fcAntibAntibIDNameIsDumpRecordDtUserID (FK)
fcAntib_LotNumAntibID (FK)LotNumCatalogNumManufacturerStartDtEndDtRecordDtUserID (FK)
fcFluorochromeFluorochromeIDNameRecordDtUserID (FK)
fcGateGateIDNameRecordDtUserID (FK)
fcMatrixMatrixIDNoOfColorsLabelRecordDtUserID (FK)
fcMatrix_ComponentsMatrixID (FK)OrdinalStateRecordDtUserID (FK)
fcMGFileCoreSampleID (FK)PanelID (FK)
FilenameArchiveID (FK)ContentRecordDtUserID (FK)
fcPanelPanelIDTestID (FK)HasMGFileRecordDtUserID (FK)
fcPanel_ComponentsPanelID (FK)TubeID (FK)TrtID (FK)GateID (FK)StartDtName (FK)OrdinalEndDtCommentsRecordDtUserID (FK)
fcRegionRegionIDNameRecordDtUserID (FK)
fcRegion_Matrix_StandardNoOfColorsRegionID (FK)MatrixID (FK)RecordDtUserID (FK)
fcResultCoreSampleID (FK)PanelID (FK)TubeID (FK)TrtID (FK)GateID (FK)RegionID (FK)MeasureID (FK)Name (FK)ValueRecordDtUserID (FK)
fcSFileCoreSampleID (FK)PanelID (FK)TubeID (FK)TrtID (FK)GateID (FK)Name (FK)FilenameArchiveID (FK)ContentRecordDtUserID (FK)
fcTrtNameTrtIDRecordDtUserID (FK)
fcTubeTubeID
TubeTypeID (FK)NameNoOfColorsRecordDtUserID (FK)
fcTube_Components
AntibID (FK)TubeID (FK)FluorochromeID (FK)OrdinalRecordDtUserID (FK)
fcTube_Region_MatrixTubeID (FK)RegionID (FK)MatrixID (FK)RecordDtUserID (FK)
fcTubeTypeTubeTypeIDNameRecordDtUserID (FK)
FieldFieldIDNameDescriptionRecordDtUserID (FK)
FileRequestRequestIDRequestDtCompletedDtEmailAddressStatusFileNameFileTypeMessageArchiveID (FK)UserName
FileRequestList
FileRequestListIDStatusFileNameDirectoryRequestID (FK)Message
LabTypeLabTypeIDNameDescriptionRecordDtUserID (FK)
Loc
LocationLocationIDNameOrganizationAddress1Address2CityStateZipRegionCountryRecordDtUserID (FK)
MeasureMeasureIDNameAbbreviationRecordDtUserID (FK)
pcrBaseVisitBaseVisitIDStudyID (FK)VisitID (FK)RecordDtUserID (FK)
pcrBatchBatchIdBatchNumberStudyID (FK)ShipDateRecordDtUserID (FK)
pcrComparison
ComparisonIDOligoID (FK)BaseMethodThresholdRecordDtUserID (FK)
pcrOligoOligoIDNameSeqAcsDescriptionClassificationRecordDtUserID (FK)
pcrQCData
QCDataIDReportNameBatchIDFilenameArchiveID (FK)RecordDTUserID (FK)
pcrReplicateReplicateIDSetID (FK)OligoID (FK)ComparisonID (FK)WellID (FK)CalibratorSampleCalibratorPlateRecordDtOperatorID
pcrResult
CoreSampleId (FK)TestID (FK)ReplicateIDBaseVisitID (FK)MeasureID (FK)ValueRecordDtUserID (FK)
pcrResult_Qual
CoreSampleid (FK)TestID (FK)ReplicateIDBaseVisitID (FK)QualifierAtLeastSampleQualityCalibratorQualityRecordDtUserID (FK)
pcrSDSFile
CoreSampleID (FK)SetID (FK)TestID (FK)ArchiveID (FK)FilenameRecordDtUserID (FK)
pcrSet
SetIDBatchIDCoreSampleID (FK)SetNamePlateBarcodeInstrumentBarcodeRecordDtAnalysisDtUserID (FK)
pcrWellWellIDWellPositionRecordDtOperatorID
Process
ProcessIDNameRecordDtUserID (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_QuQueryStudyQuerySite_qQueryQueryQueryQueryDate_Date_Date_InitiatResolExternResolDate_Query
SourceSourceIDCoreID (FK)VersionDescriptionStartDtEndDtRecordDtUserID (FK)
Source_FieldsSourceFieldID
SourceID (FK)FieldID (FK)OrdinalRecordDtSkipFlagRecordDtUserID (FK)
SampleTypeSampleTypeIDNameRecordDtUserID (FK)
ScheduleTypeScheduleTypeIDNameRecordDtUserID (FK)
SiteSiteIDShortNameStudyID (FK)LocationID (FK)CodeConvNumIsLocalLabIRBApprovedlDtITNApprovedDtBudgetApprovedDtActivationDtRecordDtUserID (FK)
StudyStudyIDStudyNumShortTitleLongTitleStartDtPhaseTherapeuticAreaID (FK)NoOfParticipantsStudyTypeID (FK)IsApprovedIsOpenDurationMoFollowUpMoAccrualMoNoEnrolledNoExtensionTreatmentPlanStateStudyStatusIDRecordDtUserID (FK)
Study_AStudAssaSpecRecoUser
Study_StuConLocUseRec
Stu
StudyTypeStudyTypeIDNameRecordDtUserID (FK)
SubjectSubjectIDSiteID (FK)ParticipantIDStudyGroupID (FK)RecordDtUserID (FK)
TestResultCoreSampleID (FK)TestID (FK)MeasureID (FK)ValueRecordDtUserID (FK)
TherapeuticArea
TherapeuticAreaIDNameRecordDtUserID (FK)
TransactionCode
TransactionCodeIDCodeDescriptionRecordDtUserID (FK)
ValidationCodeValidationCodeIDCodeDescriptionRecordDtUserID (FK)
VisitVisitIDStudyID (FK)ScheduleTypeId (FK)OrdinalVisitNumDescriptionRecordDtUserID (FK)
TestTestIDStudyID (FK)AssayID (FK)LabTypeID (FK)NameRecordDtUserID (FK)
rptDataExtractRequestRequestNumber
DtOfRequestDtRequiredByRequestorNameRequestorPhoneStudyNumCoreStudyDataQCSamplesResearchDevelopmentStartDtEndDtVisitsDetailDataFormatIncludeDeviationCodesIncludeTrtCohortIncludeUnvalidatedSamplesSpecialInstructionsAssignedToAssignedDtPlanStatusDtPlanAvailableDtPlanFinalRequestClosedByClosedDtSiteDetailsInformaticsNoteRecUpdatedByRecUpdatedOnDataExtractType
StudyStatusStudyStatusIDDescriptionRecordDtUserID (FK)
fcPanel_MeasuresPanelID (FK)TubeID (FK)TrtID (FK)GateID (FK)MeasureID (FK)Name (FK)StartDtEndDtRecordDtUserID (FK)
EnrollmentEnrollmentIDSiteID (FK)ScreeningIDParticipantIDScreeningDtEnrollmentDtStudyGroupID (FK)DonorIDRecipientIDRecordDtScreeningFailureResasonIDScreeningFailureCommentUserID (FK)
ETLMappingDetailMapDtlIDSourceColumnTargetTableTargetColumnTypeMapHdrID
ETLMappingHeaderMapHdrIDMappingNameSourceVersion
GenericLoadGenLoadIDFileNameFileDirRowNumberColumnNameCellValueSourceVersiondtEnteredLoadID
GenericLoadBatchGLBatchIDFileDirRecordDtFileName
HLABusinessRuleDetailBRDetailIDTargetTableTargetColumnBRValueTargetColumnTypeBRHdrID
HLABusinessRuleHeaderBRHdrIDVersionBRName
HLADataImportLogImportLogID
FileNameStudyNumCodeVisitNumSpecimenTypeParticipantIDBarcodeDescriptionRecordDtOperatorIDAccessionID
HLAEvertLogHLAEventLogIDEventDescRecordDtOperatorIDGLBatchID
HLAResultHLAResultIDA_1A_2B_1B_2Cw_1Cw_2DRB1_1DRB1_2DRB3_1DRB3_2DRB4_1DRB4_2DRB5_1DRB5_2DQA1_1DQA1_2DQB1_1DQB1_2HLACommentsHLAComments_AnalysisRecordDtOperatorIDCoreSampleID
ScreeningFailureReasonScreeningFailureReasonIDCodeDescriptionEnabledStudyID
TransplantTransplantIdRecipient_SubjectIdDonor_SubjectIdOrganRecordDtOperatorStudyId
Transplant
Visit 0
0
v 0
v0
Day 0
What is in a visit name?
ITN_BioMed V5Schema
AccessionAccessionIDCoreID (FK)FilenameTransmissionDtTransactionCodeID (FK)RecordDtUserID (FK)
ArchiveArchiveIDCoreID (FK)ProcessID (FK)NameDirectoryRecordDtUserID (FK)
BarcodeBarcodeIDStudyID (FK)SubjectID (FK)VisitID (FK)BarcodeCollectionDtRecordDtUserID (FK)
ConfigParameterConfigParameterIDProcessID (FK)NameValueRecordDtUserID (FK)
ContactTypeContactTypeIDNameRecordDtUserID (FK)
Core
CoreIDLocationID (FK)CodeDescriptionRecordDtUserID (FK)
Core_AssaysCoreID (FK)AssayID (FK)SpecimenTypeID (FK)RecordDtUserID (FK)
Core_ContactsCoreID (FK)ContactTypeID (FK)UserID (FK)RecordDt
Core_IssuesIssueIDCoreStudyCoresampleIDRequestedByDescriptionRequestDtResponseStatusCoreSampleID (FK)
CoreSampleCoreSampleIDStudyID (FK)AccessionID (FK)ProcessingCodeID (FK)SampleTypeID (FK)RecdDtAnalysisDtTechnameFilenameExternalIDBarcodeID9SpecimenTypeID (FK)RecordDtUserID (FK)
CoreSample_DetailCoreSampleID (FK)BarcodeID (FK)QCSampleID (FK)ValidationCodeID (FK)ValidationDtRecordDtUserID (FK)
CoreSample_DevCodeCoreSampleID (FK)DevCodeID (FK)NotesRecordDtUserID (FK)
DevCodeDevCodeID
CodeDescriptionGetCommentsRecordDtUserID (FK)
fcAntibAntibIDNameIsDumpRecordDtUserID (FK)
fcAntib_LotNumAntibID (FK)LotNumCatalogNumManufacturerStartDtEndDtRecordDtUserID (FK)
fcFluorochromeFluorochromeIDNameRecordDtUserID (FK)
fcGateGateIDNameRecordDtUserID (FK)
fcMatrixMatrixIDNoOfColorsLabelRecordDtUserID (FK)
fcMatrix_ComponentsMatrixID (FK)OrdinalStateRecordDtUserID (FK)
fcMGFileCoreSampleID (FK)PanelID (FK)
FilenameArchiveID (FK)ContentRecordDtUserID (FK)
fcPanelPanelIDTestID (FK)HasMGFileRecordDtUserID (FK)
fcPanel_ComponentsPanelID (FK)TubeID (FK)TrtID (FK)GateID (FK)StartDtName (FK)OrdinalEndDtCommentsRecordDtUserID (FK)
fcRegionRegionIDNameRecordDtUserID (FK)
fcRegion_Matrix_StandardNoOfColorsRegionID (FK)MatrixID (FK)RecordDtUserID (FK)
fcResultCoreSampleID (FK)PanelID (FK)TubeID (FK)TrtID (FK)GateID (FK)RegionID (FK)MeasureID (FK)Name (FK)ValueRecordDtUserID (FK)
fcSFileCoreSampleID (FK)PanelID (FK)TubeID (FK)TrtID (FK)GateID (FK)Name (FK)FilenameArchiveID (FK)ContentRecordDtUserID (FK)
fcTrtNameTrtIDRecordDtUserID (FK)
fcTubeTubeID
TubeTypeID (FK)NameNoOfColorsRecordDtUserID (FK)
fcTube_Components
AntibID (FK)TubeID (FK)FluorochromeID (FK)OrdinalRecordDtUserID (FK)
fcTube_Region_MatrixTubeID (FK)RegionID (FK)MatrixID (FK)RecordDtUserID (FK)
fcTubeTypeTubeTypeIDNameRecordDtUserID (FK)
FieldFieldIDNameDescriptionRecordDtUserID (FK)
FileRequestRequestIDRequestDtCompletedDtEmailAddressStatusFileNameFileTypeMessageArchiveID (FK)UserName
FileRequestList
FileRequestListIDStatusFileNameDirectoryRequestID (FK)Message
LabTypeLabTypeIDNameDescriptionRecordDtUserID (FK)
Loc
LocationLocationIDNameOrganizationAddress1Address2CityStateZipRegionCountryRecordDtUserID (FK)
MeasureMeasureIDNameAbbreviationRecordDtUserID (FK)
pcrBaseVisitBaseVisitIDStudyID (FK)VisitID (FK)RecordDtUserID (FK)
pcrBatchBatchIdBatchNumberStudyID (FK)ShipDateRecordDtUserID (FK)
pcrComparison
ComparisonIDOligoID (FK)BaseMethodThresholdRecordDtUserID (FK)
pcrOligoOligoIDNameSeqAcsDescriptionClassificationRecordDtUserID (FK)
pcrQCData
QCDataIDReportNameBatchIDFilenameArchiveID (FK)RecordDTUserID (FK)
pcrReplicateReplicateIDSetID (FK)OligoID (FK)ComparisonID (FK)WellID (FK)CalibratorSampleCalibratorPlateRecordDtOperatorID
pcrResult
CoreSampleId (FK)TestID (FK)ReplicateIDBaseVisitID (FK)MeasureID (FK)ValueRecordDtUserID (FK)
pcrResult_Qual
CoreSampleid (FK)TestID (FK)ReplicateIDBaseVisitID (FK)QualifierAtLeastSampleQualityCalibratorQualityRecordDtUserID (FK)
pcrSDSFile
CoreSampleID (FK)SetID (FK)TestID (FK)ArchiveID (FK)FilenameRecordDtUserID (FK)
pcrSet
SetIDBatchIDCoreSampleID (FK)SetNamePlateBarcodeInstrumentBarcodeRecordDtAnalysisDtUserID (FK)
pcrWellWellIDWellPositionRecordDtOperatorID
Process
ProcessIDNameRecordDtUserID (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_QuQueryStudyQuerySite_qQueryQueryQueryQueryDate_Date_Date_InitiatResolExternResolDate_Query
SourceSourceIDCoreID (FK)VersionDescriptionStartDtEndDtRecordDtUserID (FK)
Source_FieldsSourceFieldID
SourceID (FK)FieldID (FK)OrdinalRecordDtSkipFlagRecordDtUserID (FK)
SampleTypeSampleTypeIDNameRecordDtUserID (FK)
ScheduleTypeScheduleTypeIDNameRecordDtUserID (FK)
SiteSiteIDShortNameStudyID (FK)LocationID (FK)CodeConvNumIsLocalLabIRBApprovedlDtITNApprovedDtBudgetApprovedDtActivationDtRecordDtUserID (FK)
StudyStudyIDStudyNumShortTitleLongTitleStartDtPhaseTherapeuticAreaID (FK)NoOfParticipantsStudyTypeID (FK)IsApprovedIsOpenDurationMoFollowUpMoAccrualMoNoEnrolledNoExtensionTreatmentPlanStateStudyStatusIDRecordDtUserID (FK)
Study_AStudAssaSpecRecoUser
Study_StuConLocUseRec
Stu
StudyTypeStudyTypeIDNameRecordDtUserID (FK)
SubjectSubjectIDSiteID (FK)ParticipantIDStudyGroupID (FK)RecordDtUserID (FK)
TestResultCoreSampleID (FK)TestID (FK)MeasureID (FK)ValueRecordDtUserID (FK)
TherapeuticArea
TherapeuticAreaIDNameRecordDtUserID (FK)
TransactionCode
TransactionCodeIDCodeDescriptionRecordDtUserID (FK)
ValidationCodeValidationCodeIDCodeDescriptionRecordDtUserID (FK)
VisitVisitIDStudyID (FK)ScheduleTypeId (FK)OrdinalVisitNumDescriptionRecordDtUserID (FK)
TestTestIDStudyID (FK)AssayID (FK)LabTypeID (FK)NameRecordDtUserID (FK)
rptDataExtractRequestRequestNumber
DtOfRequestDtRequiredByRequestorNameRequestorPhoneStudyNumCoreStudyDataQCSamplesResearchDevelopmentStartDtEndDtVisitsDetailDataFormatIncludeDeviationCodesIncludeTrtCohortIncludeUnvalidatedSamplesSpecialInstructionsAssignedToAssignedDtPlanStatusDtPlanAvailableDtPlanFinalRequestClosedByClosedDtSiteDetailsInformaticsNoteRecUpdatedByRecUpdatedOnDataExtractType
StudyStatusStudyStatusIDDescriptionRecordDtUserID (FK)
fcPanel_MeasuresPanelID (FK)TubeID (FK)TrtID (FK)GateID (FK)MeasureID (FK)Name (FK)StartDtEndDtRecordDtUserID (FK)
EnrollmentEnrollmentIDSiteID (FK)ScreeningIDParticipantIDScreeningDtEnrollmentDtStudyGroupID (FK)DonorIDRecipientIDRecordDtScreeningFailureResasonIDScreeningFailureCommentUserID (FK)
ETLMappingDetailMapDtlIDSourceColumnTargetTableTargetColumnTypeMapHdrID
ETLMappingHeaderMapHdrIDMappingNameSourceVersion
GenericLoadGenLoadIDFileNameFileDirRowNumberColumnNameCellValueSourceVersiondtEnteredLoadID
GenericLoadBatchGLBatchIDFileDirRecordDtFileName
HLABusinessRuleDetailBRDetailIDTargetTableTargetColumnBRValueTargetColumnTypeBRHdrID
HLABusinessRuleHeaderBRHdrIDVersionBRName
HLADataImportLogImportLogID
FileNameStudyNumCodeVisitNumSpecimenTypeParticipantIDBarcodeDescriptionRecordDtOperatorIDAccessionID
HLAEvertLogHLAEventLogIDEventDescRecordDtOperatorIDGLBatchID
HLAResultHLAResultIDA_1A_2B_1B_2Cw_1Cw_2DRB1_1DRB1_2DRB3_1DRB3_2DRB4_1DRB4_2DRB5_1DRB5_2DQA1_1DQA1_2DQB1_1DQB1_2HLACommentsHLAComments_AnalysisRecordDtOperatorIDCoreSampleID
ScreeningFailureReasonScreeningFailureReasonIDCodeDescriptionEnabledStudyID
TransplantTransplantIdRecipient_SubjectIdDonor_SubjectIdOrganRecordDtOperatorStudyId
Transplant
Visit 0
0
v 0
v0
Day 0
What is in a visit name?How many participants
have had transplants so far and what are the results of
the assays performed at the time of transplant?
Challenges in Trials Management
Enterprise-wide knowledge about trials management is not formally encoded, leading to challenges in• Standardization• Data integrity• Data analysis• Data integration
Significant efforts may be needed to resolve inconsistencies after a trial has started
ITN Informatics Core at Stanford
EpochAn Ontological Framework for Clinical
Trials Management
ITN Informatics Core at Stanford
The goals of our collaboration are toDesign tools to help acquire and maintain knowledge about protocol and assay designsUse this knowledge to drive data collection during a trialImplement querying methods to support trial management, and ad hoc data analysis
Building Ontologies for ITN — Epoch
RT PCRCore
KidneyCore
1 x cryovial(kidney)
1 x cryomold(kidney)
1 x cryovial(kidney)
–E21
1 x 0.5ml cryovial(kidney RNA)
1 x 0.5 cryovial(kidney RNA)
1 x cryomold(kidney)
Barcode Suffix – E22
FisherLab
RNA ProcessingCore
SpecimenDisposalPoint
1 x cryovial(kidney)
1 x cryomold(kidney)
1 x cryovial(kidney)
Barcode Suffix –E21
1 x 0.5ml cryovial(kidney RNA)
1 x 0.5 cryovial(kidney RNA)
1 x cryomold(kidney)
Barcode Suffix – E22
SpecimenCollectionPoint
Building Ontologies for ITN — Epoch
Epoch
CDISCBRIDG
EONSAGE
ITNspecifications
Epoch Ontologies
ProtocolModel
Epoch Ontologies
ProtocolModel
Protocol Schema
Mechanistic Study Plan
Epoch Ontologies
ProtocolModel
Protocol Schema
Mechanistic Study Plan
ActivityVisit
Epoch Ontologies
ProtocolModel
Protocol Schema
Mechanistic Study Plan
ClinicalModel
ActivityVisit
Epoch Ontologies
ProtocolModel
Protocol Schema
ClinicalModel
ActivityVisit
Mechanistic Study Plan
SpecimenWorkflow
SpecimenContainer
Set
Assay
Epoch Ontologies
ProtocolModel
Protocol Schema
ClinicalModel
ActivityVisit
Mechanistic Study Plan
AssayModel
SpecimenWorkflow
SpecimenContainer
Set
Assay
Epoch Ontologies
ProtocolModel
Protocol Schema
ClinicalModel
ActivityVisit
Mechanistic Study Plan
AssayModel
SpecimenContainer
Model
SpecimenWorkflow Site
Model
SpecimenContainer
Set
Assay
Epoch Ontologies
ProtocolModel
Protocol Schema
Mechanistic Study Plan
AssayModel
SpecimenContainer
Model
SpecimenWorkflow Site
Model
SpecimenContainer
Set
ClinicalModel
Activity
Assay Virtual TrialData
Model
Visit
Knowledge-Acquisition Environment
OWL (the Web Ontology Language proposed by W3C)
SWRL (the Semantic Web Rule Language) to specify constraints and queries
Protégé-OWL editor to enter ontologies in OWL and SWRL
Epoch Protocol Model
Epoch Protocol Model
Schedule of Events
Visit
Period
TimeAnchor
Annotation
TemporalConstraint
Activity
Protocol Model – Study Schema
Study Schema
Study Schema – a Temporal Sequence of Periods
Visit Flow – a Temporal Sequence of Visits
Visit
Visit – different Visit names
Specimen Table
Assay
ProcessingInstruction
MechanisticStudy
Specimen Workflow
Specimen Container
Protocol Model - Mechanistic Study Plan
Mechanistic Study Plan
Mechanistic Study Plan
Mechanistic Study Plan
A Mechanistic Study
A Mechanistic Study
Specimen Workflow
Specimen Workflow
Mechanistic Study Plan
Specimen Container Set
Specimen Container Set
Specimen Container Set
Specimen Container Set
Specimen Container Ontology – using OWL Full meta model
Specimen Container Ontology – using OWL Full meta model
Specimen Container Ontology – using OWL Full meta model
Specimen Container Ontology
A Hierarchy of Specimen Containers
A Specimen Container
Assay Ontology – using OWL Full meta model
Assay Ontology – using OWL Full meta model
Assay Ontology
Assay Ontology
An Assay
Virtual Trial Data Model - Observation
Virtual Trial Data Model - VisitRecord
Anchor Point - Transplant
SWRL Rule to set Transplant Time
Visit Time Window
Visit Time constraint as a SWRL rule
Check if the participant's visits occurred within the visit time window specifications
Constraints expressed as SWRL rules
On days that both immunotherapy and omalizumab are administered, omalizumab will be injected 60 minutes after the immunotherapy.
ITN Informatics Core at Stanford
The goals of our collaboration are toDesign tools to help acquire and maintain knowledge about protocol and assay designsUse this knowledge to drive data collection during a trialImplement querying methods to support trial monitoring, protocol tracking, and ad hoc data analysis
Epoch Architectural Plan
Epoch Knowledge Base
OWL | SWRL
Epoch Architectural Plan
Epoch Knowledge Base
Knowledge Base Server
OWL | SWRL
API
Epoch Architectural Plan
Epoch Knowledge Base
Knowledge Base Server
Clinical Trial
Database
Model-Database Mapper
OWL | SWRL
API
Epoch Architectural Plan
Epoch Knowledge Base
Knowledge Base Server
Clinical Trial
Database
Model-Database Mapper
Query / Rule Engine
SWRL | JESS
OWL | SWRL
API
Epoch Architectural Plan
Epoch Knowledge Base
Knowledge Base Server
Clinical Trial
Database
Model-Database Mapper
Query / Rule Engine
SWRL | JESS
OWL | SWRL
API
Utility Functions
Epoch Architectural Plan
Epoch Knowledge Base
Knowledge Base Server
Clinical Trial
Database
Model-Database Mapper
Clinical Trials Management Applications
Query / Rule Engine
SWRL | JESS
OWL | SWRL
API
Utility Functions
Configuration of ImmunoTrak – the Specimen Workflow Application
ImmunoTrak Configuration File
Configuration of ImmunoTrak – the Specimen Workflow Application
Epoch Knowledge Base
ImmunoTrak Configuration
ImmunoTrak ―Specimen Workflow
12
Ontology Mapping to generate XML Document
Epoch Ontology
ImmunoTrak Configuration XML
Protocol(?p) ^ hasSitePlan(?p, ?sp) ^ hasStudySites(?sp, ?site) ^ hasSiteID(?site, ?siteID) ^ hasParticipant(?site, ?participants) ^ hasParticipantIDs(?participant, ?participantID) ^ hasStudyInformation(?sp, ?studyInfo) ^ hasStudyID(?studyInfo, ?hasStudyID) -> XMLDocument(?p) ^ hasNodeName(?p, "Study") ^ XMLComponent(?participant) ^ hasNodeName(?participant, "Participant") ^ hasComponents(?p, ?participant) ^ hasAttribute(?participant, ?participantID) ^ hasAttributeName(?participantID, "id">
XML Document Ontology
SWRL
ProtégéOWL
ClinicalOntology
GenericProtocolModel
AssayOntology
SiteOntology
ElectronicCRF
ParticipantVisits
SpecimenIdentification
SpecimenWorkflow
ProtocolProtocolProtocol+Specimen
Table
Applications forKnowledge Specification
Applications forData Collection
Applications forClinical TrialsManagement
CRF
Tracking
Core
DataRepository
ProtocolProtocolSpecificAssays
ProtocolProtocolSpecificSites
EpochOntologies
ContainerOntology
ProtocolProtocolSpecificKits
What our approach buys us
A centralized, modifiable repository of the knowledge to drive site-oriented applicationsThe ability to use reference ontologies to structure ITN knowledgeA scaleable architecture that can lead to computer-supported trial design The ability to use logic for inferring relationships among the data