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)


–E21

1 x 0.5ml cryovial(kidney RNA)

1 x 0.5 cryovial(kidney RNA)


Barcode Suffix – E22

FisherLab

RNA ProcessingCore

SpecimenDisposalPoint




Barcode Suffix –E21





SpecimenCollectionPoint

RT PCRCore

KidneyCore




–E21





FisherLab

RNA ProcessingCore










SiteLab

Core lab

Bio-RepositorySpecimen

Container

Specimen Workflow


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


ProtocolGroup

Assay Group

0

0

Schedule of Events

SpecimenTable


ProtocolGroup

Assay Group

CRO Day 0, Transplant

0

0

CRF

Schedule of Events

SpecimenTable


ProtocolGroup

Assay Group

OperationsGroup

CRO

v 0

0

0

Day 0, Transplant

TubeTable

CRF

Schedule of Events

SpecimenTable


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


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


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


ArchiveArchiveIDCoreID (FK)ProcessID (FK)NameDirectoryRecordDtUserID (FK)



ContactTypeContactTypeIDNameRecordDtUserID (FK)

Core

CoreIDLocationID (FK)CodeDescriptionRecordDtUserID (FK)



Core_IssuesIssueIDCoreStudyCoresampleIDRequestedByDescriptionRequestDtResponseStatusCoreSampleID (FK)

CoreSampleCoreSampleIDStudyID (FK)AccessionID (FK)ProcessingCodeID (FK)SampleTypeID (FK)RecdDtAnalysisDtTechnameFilenameExternalIDBarcodeID9SpecimenTypeID (FK)RecordDtUserID (FK)



DevCodeDevCodeID


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)



FileRequestList


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


pcrSDSFile

CoreSampleID (FK)SetID (FK)TestID (FK)ArchiveID (FK)FilenameRecordDtUserID (FK)

pcrSet

SetIDBatchIDCoreSampleID (FK)SetNamePlateBarcodeInstrumentBarcodeRecordDtAnalysisDtUserID (FK)

pcrWellWellIDWellPositionRecordDtOperatorID

Process



SMS_Acc




SMS_QuQueryStudyQuerySite_qQueryQueryQueryQueryDate_Date_Date_InitiatResolExternResolDate_Query

SourceSourceIDCoreID (FK)VersionDescriptionStartDtEndDtRecordDtUserID (FK)




ScheduleTypeScheduleTypeIDNameRecordDtUserID (FK)

SiteSiteIDShortNameStudyID (FK)LocationID (FK)CodeConvNumIsLocalLabIRBApprovedlDtITNApprovedDtBudgetApprovedDtActivationDtRecordDtUserID (FK)

StudyStudyIDStudyNumShortTitleLongTitleStartDtPhaseTherapeuticAreaID (FK)NoOfParticipantsStudyTypeID (FK)IsApprovedIsOpenDurationMoFollowUpMoAccrualMoNoEnrolledNoExtensionTreatmentPlanStateStudyStatusIDRecordDtUserID (FK)

Study_AStudAssaSpecRecoUser

Study_StuConLocUseRec

Stu

StudyTypeStudyTypeIDNameRecordDtUserID (FK)


TestResultCoreSampleID (FK)TestID (FK)MeasureID (FK)ValueRecordDtUserID (FK)

TherapeuticArea

TherapeuticAreaIDNameRecordDtUserID (FK)

TransactionCode



VisitVisitIDStudyID (FK)ScheduleTypeId (FK)OrdinalVisitNumDescriptionRecordDtUserID (FK)

TestTestIDStudyID (FK)AssayID (FK)LabTypeID (FK)NameRecordDtUserID (FK)



StudyStatusStudyStatusIDDescriptionRecordDtUserID (FK)

fcPanel_MeasuresPanelID (FK)TubeID (FK)TrtID (FK)GateID (FK)MeasureID (FK)Name (FK)StartDtEndDtRecordDtUserID (FK)

EnrollmentEnrollmentIDSiteID (FK)ScreeningIDParticipantIDScreeningDtEnrollmentDtStudyGroupID (FK)DonorIDRecipientIDRecordDtScreeningFailureResasonIDScreeningFailureCommentUserID (FK)




GenericLoadBatchGLBatchIDFileDirRecordDtFileName






HLAResultHLAResultIDA_1A_2B_1B_2Cw_1Cw_2DRB1_1DRB1_2DRB3_1DRB3_2DRB4_1DRB4_2DRB5_1DRB5_2DQA1_1DQA1_2DQB1_1DQB1_2HLACommentsHLAComments_AnalysisRecordDtOperatorIDCoreSampleID



Transplant

Visit 0

0

v 0

v0

Day 0

What is in a visit name?

ITN_BioMed V5Schema


ArchiveArchiveIDCoreID (FK)ProcessID (FK)NameDirectoryRecordDtUserID (FK)



ContactTypeContactTypeIDNameRecordDtUserID (FK)

Core

CoreIDLocationID (FK)CodeDescriptionRecordDtUserID (FK)



Core_IssuesIssueIDCoreStudyCoresampleIDRequestedByDescriptionRequestDtResponseStatusCoreSampleID (FK)

CoreSampleCoreSampleIDStudyID (FK)AccessionID (FK)ProcessingCodeID (FK)SampleTypeID (FK)RecdDtAnalysisDtTechnameFilenameExternalIDBarcodeID9SpecimenTypeID (FK)RecordDtUserID (FK)



DevCodeDevCodeID


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)



FileRequestList


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


pcrSDSFile

CoreSampleID (FK)SetID (FK)TestID (FK)ArchiveID (FK)FilenameRecordDtUserID (FK)

pcrSet

SetIDBatchIDCoreSampleID (FK)SetNamePlateBarcodeInstrumentBarcodeRecordDtAnalysisDtUserID (FK)

pcrWellWellIDWellPositionRecordDtOperatorID

Process



SMS_Acc




SMS_QuQueryStudyQuerySite_qQueryQueryQueryQueryDate_Date_Date_InitiatResolExternResolDate_Query

SourceSourceIDCoreID (FK)VersionDescriptionStartDtEndDtRecordDtUserID (FK)




ScheduleTypeScheduleTypeIDNameRecordDtUserID (FK)

SiteSiteIDShortNameStudyID (FK)LocationID (FK)CodeConvNumIsLocalLabIRBApprovedlDtITNApprovedDtBudgetApprovedDtActivationDtRecordDtUserID (FK)

StudyStudyIDStudyNumShortTitleLongTitleStartDtPhaseTherapeuticAreaID (FK)NoOfParticipantsStudyTypeID (FK)IsApprovedIsOpenDurationMoFollowUpMoAccrualMoNoEnrolledNoExtensionTreatmentPlanStateStudyStatusIDRecordDtUserID (FK)

Study_AStudAssaSpecRecoUser

Study_StuConLocUseRec

Stu

StudyTypeStudyTypeIDNameRecordDtUserID (FK)


TestResultCoreSampleID (FK)TestID (FK)MeasureID (FK)ValueRecordDtUserID (FK)

TherapeuticArea

TherapeuticAreaIDNameRecordDtUserID (FK)

TransactionCode



VisitVisitIDStudyID (FK)ScheduleTypeId (FK)OrdinalVisitNumDescriptionRecordDtUserID (FK)

TestTestIDStudyID (FK)AssayID (FK)LabTypeID (FK)NameRecordDtUserID (FK)



StudyStatusStudyStatusIDDescriptionRecordDtUserID (FK)

fcPanel_MeasuresPanelID (FK)TubeID (FK)TrtID (FK)GateID (FK)MeasureID (FK)Name (FK)StartDtEndDtRecordDtUserID (FK)

EnrollmentEnrollmentIDSiteID (FK)ScreeningIDParticipantIDScreeningDtEnrollmentDtStudyGroupID (FK)DonorIDRecipientIDRecordDtScreeningFailureResasonIDScreeningFailureCommentUserID (FK)




GenericLoadBatchGLBatchIDFileDirRecordDtFileName






HLAResultHLAResultIDA_1A_2B_1B_2Cw_1Cw_2DRB1_1DRB1_2DRB3_1DRB3_2DRB4_1DRB4_2DRB5_1DRB5_2DQA1_1DQA1_2DQB1_1DQB1_2HLACommentsHLAComments_AnalysisRecordDtOperatorIDCoreSampleID



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


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




–E21





FisherLab

RNA ProcessingCore











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


ActivityVisit

Epoch Ontologies

ProtocolModel

Protocol Schema


ClinicalModel

ActivityVisit

Epoch Ontologies

ProtocolModel

Protocol Schema

ClinicalModel

ActivityVisit


SpecimenWorkflow

SpecimenContainer

Set

Assay

Epoch Ontologies

ProtocolModel

Protocol Schema

ClinicalModel

ActivityVisit


AssayModel

SpecimenWorkflow

SpecimenContainer

Set

Assay

Epoch Ontologies

ProtocolModel

Protocol Schema

ClinicalModel

ActivityVisit


AssayModel

SpecimenContainer

Model

SpecimenWorkflow Site

Model

SpecimenContainer

Set

Assay

Epoch Ontologies

ProtocolModel

Protocol Schema


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

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 – different Visit names

Specimen Table

Assay

ProcessingInstruction

MechanisticStudy

Specimen Workflow

Specimen Container

Protocol Model - Mechanistic Study Plan

A Mechanistic Study

Specimen Workflow

Specimen Container Set

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

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.


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



Knowledge Base Server

OWL | SWRL

API




Clinical Trial

Database

Model-Database Mapper

OWL | SWRL

API




Clinical Trial

Database


Query / Rule Engine

SWRL | JESS

OWL | SWRL

API




Clinical Trial

Database


Query / Rule Engine

SWRL | JESS

OWL | SWRL

API

Utility Functions




Clinical Trial

Database


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


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

epoch ontological framework to support clinical … ontological framework to support clinical trial...

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