[PPT] - Epoch Ontological Framework to support Clinical Trial Management PowerPoint Presentation

SLIDE 1

Epoch Ontological Framework to support Clinical Trial Management

Ravi Shankar Stanford Medical Informatics Stanford University

SLIDE 2

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.

SLIDE 3

The Immune Tolerance Network

ITN is an international collaboration designed to

accelerate the development of immune tolerance therapies

Funds, plans, implements, monitors, and assesses

investigator-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

SLIDE 4

Schedule of Events

SLIDE 5

Schedule of Events

Visit Period Time Anchor Annotation Temporal Constraint Activity

SLIDE 6

Specimen Table

SLIDE 7

Specimen Table

Assay Processing Instruction Mechanistic Study Specimen Workflow Specimen Container

SLIDE 8

Specimen Workflow

RT PCR Core Kidney Core

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

Fisher Lab RNA Processing Core

Specimen Disposal Point

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

Specimen Collection Point

SLIDE 9

RT PCR Core Kidney Core

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

Fisher Lab RNA Processing Core

Specimen Disposal Point

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

Site Lab Core lab Bio- Repository Specimen Container

Specimen Workflow

Specimen Collection Point

SLIDE 10

Challenges in Trials Management

Knowledge about protocols, assays,

and specimen flow is captured in documents and spreadsheets

Plan Implement Monitor Assess Core CRF Tracking

SLIDE 11

What is in a visit name? Visit 0, v0, v 0, 0, Day 0, Transplant

SLIDE 12

What is in a visit name? Visit 0, v0, v 0, 0, Day 0, Transplant

Protocol Group Assay Group

Schedule

f Events

Specim en Table

SLIDE 13

What is in a visit name? Visit 0, v0, v 0, 0, Day 0, Transplant

Protocol Group Assay Group CRO Day 0 , Transplant

CRF Schedule

f Events

Specim en Table

SLIDE 14

What is in a visit name? Visit 0, v0, v 0, 0, Day 0, Transplant

Protocol Group Assay Group Operations Group CRO

v 0

Day 0 , Transplant

Tube Table CRF Schedule

f Events

Specim en Table

SLIDE 15

What is in a visit name? Visit 0, v0, v 0, 0, Day 0, Transplant

Protocol Group Assay Group Operations Group CRO Cim arron Fisher

Kit Report

Day 0 , Transplant

v 0 v 0 v0 , Visit 0

I m m unoTrak CRF Tube Table Schedule

f Events

Specim en Table

SLIDE 16

What is in a visit name? Visit 0, v0, v 0, 0, Day 0, Transplant

Protocol Group Assay Group Operations Group Fisher Core Labs CRO Cim arron Day 0 , Transplant

v0 v0 , Visit 0 v 0 v 0

Kit Report I m m unoTrak Assays CRF Tube Table Schedule

f Events

Specim en Table

SLIDE 17

What is in a visit name? Visit 0, v0, v 0, 0, Day 0, Transplant

CRO Protocol Group Assay Group Cim arron Operations Group Data Center Core Labs Fisher Day 0 , Transplant

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SLIDE 18

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What is in a visit name?

SLIDE 19

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s Label R ecordD t U ser ID (FK ) fcMatrix_C

mponents

MatrixID (FK ) Ordinal State R ecor dD t U serID (FK ) fcMGFile C

reS

am pleID (FK ) PanelID (FK ) Filename A r chiveID (FK ) C

ntent

R ecor dD t U serID (FK ) fcP anel PanelID TestID (FK ) H asMGFile R ecor dD t U serID (FK ) fcP anel_C

m

ponents PanelID (FK ) TubeID (FK ) Tr tID (FK ) GateID (FK ) Star tD t N am e (FK ) Ordinal EndD t C

m

ments R ecor dD t U serID (FK ) fcR egion R egionID N am e R ecordD t U serID (FK ) fcR egion_Matr ix_S tandard N

OfC
lors

R egionID (FK ) MatrixID (FK ) R ecor dD t U serID (FK ) fcR esult C

reSampleID

(FK) P anelID (FK ) TubeID (FK ) TrtID (FK) GateID (FK ) R egi

nID

(FK) MeasureID (FK ) N am e (FK ) V alue R ecordD t U ser ID (FK ) fcS File C

reS

ampleID (FK ) PanelID (FK ) TubeID (FK ) Tr tID (FK ) GateID (FK ) N am e (FK ) Filenam e A r chiveID (FK ) C

ntent

R ecor dD t U serID (FK ) fcTr t N am e TrtID R ecordD t U ser ID (FK ) fcTube TubeID TubeTypeID (FK ) N am e N

OfC
lors

R ecor dD t U serID (FK ) fcTube_C

m

ponents A ntibID (FK ) TubeID (FK ) FluorochromeID (FK ) Or dinal R ecordD t U ser ID (FK ) fcTube_R egion_Matrix TubeID (FK ) R egionID (FK ) Matr ixID (FK ) R ecordD t U ser ID (FK ) fcTubeType TubeTypeID N am e R ecordD t U ser ID (FK ) Field FieldID N ame D escription R ecordD t U serID (FK ) FileR equest R equestID R equestD t C

m

pletedD t E m ailA ddress S tatus FileN am e FileType Message A rchiveID (FK ) U serN ame FileR equestList FileR equestListID Status FileN am e D irectory R equestID (FK ) Message LabType LabTypeID N ame D escription R ecordD t U ser ID (FK ) Loc Location LocationID N am e Or ganization A ddr ess1 A ddr ess2 C ity S tate Zip R egion C

untr

y R ecordD t U ser ID (FK ) Measur e MeasureID N ame A bbr eviation R ecordD t U ser ID (FK ) pcrB aseV isit B aseV isitID S tudyID (FK ) V isitID (FK ) R ecordD t U ser ID (FK ) pcrB atch B atchId B atchN umber S tudyID (FK ) S hipD ate R ecor dD t U serID (FK ) pcrC

m

parison C

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parisonID OligoID (FK ) B aseMethod Threshold R ecordD t U ser ID (FK ) pcr Oligo OligoID N am e SeqA cs D escription C lassification R ecordD t U ser ID (FK ) pcrQC D ata QC D ataID R eportN am e B atchID Filename A rchiveID (FK ) R ecordD T U ser ID (FK ) pcrR eplicate R eplicateID S etID (FK ) OligoID (FK ) C

mpar

isonID (FK ) W ellID (FK ) C alibrator Sample C alibrator Plate R ecordD t Oper atorID pcrR esult C

r

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reS

ampleid (FK ) TestID (FK ) R eplicateID B aseV isitID (FK ) Qualifier A tLeast Sam pleQuality C alibr atorQuality R ecor dD t U serID (FK ) pcrS D S File C

r

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de

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reS

ampleID (FK ) TestID (FK ) MeasureID (FK ) Value R ecor dD t U serID (FK ) Ther apeuticA r ea TherapeuticA reaID N am e R ecordD t U serID (FK ) TransactionC

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Tr ansactionC

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C

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D escr iption R ecor dD t U serID (FK ) ValidationC

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StudyD ata QC S am ples R esearchD evelopm ent StartD t EndD t VisitsD etail D ataForm at IncludeD eviationC

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R ecU pdatedB y R ecU pdatedOn D ataExtr actType StudyS tatus S tudyS tatusID D escription R ecordD t U ser ID (FK ) fcPanel_Measures P anelID (FK ) TubeID (FK ) TrtID (FK ) GateID (FK ) MeasureID (FK ) N ame (FK ) S tartD t E ndD t R ecordD t U ser ID (FK ) E nrollment E nr

llm

entID S iteID (FK ) S cr eeningID P ar ticipantID S cr eeningD t E nr

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norID

R ecipientID R ecordD t S cr eeningFailureR esasonID S cr eeningFailureC

m

ment U serID (FK ) ETLMappingD etail MapD tlID S

ur

ceC

lum

n TargetTable TargetC

lumnType

MapH drID E TLMappingH eader MapH drID MappingN ame S

urce

V er sion GenericLoad GenLoadID FileN am e FileD ir R

wN

umber C

lumnN

ame C ellValue Source Version dtEntered LoadID GenericLoadB atch GLB atchID FileD ir R ecordD t FileN ame H LA B usinessR uleD etail B R D etailID TargetTable TargetC

lumn

B R Value TargetC

lumnType

B R H drID H LA B usinessR uleH eader B R H drID V ersion B R N am e H LA D ataIm portLog Impor tLogID FileN ame StudyN um C

de

VisitN um Specim enType ParticipantID B arcode D escr iption R ecor dD t OperatorID A ccessionID H LA E ver tLog H LA E ventLogID E ventD esc R ecordD t Oper ator ID GLB atchID H LA R esult H LA R esultID A _1 A _2 B _1 B _2 C w_1 C w_2 D R B 1_1 D R B 1_2 D R B 3_1 D R B 3_2 D R B 4_1 D R B 4_2 D R B 5_1 D R B 5_2 D QA 1_1 D QA 1_2 D QB 1_1 D QB 1_2 H LA C

m

m ents H LA C

m

m ents_A nalysis R ecordD t OperatorID C

reSampleID

ScreeningFailur eR eason S creeningFailureR easonID C

de

D escription E nabled S tudyID Transplant Tr ansplantId R ecipient_S ubjectId D

nor

_S ubjectId Organ R ecor dD t Operator StudyId

Transplant

Visit 0 v 0 v0 Day 0

What is in a visit name?

How m any participants have had transplants so far and w hat are the results of the assays perform ed at the tim e of transplant?

SLIDE 20

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

SLIDE 21

ITN Informatics Core at Stanford Epoch

An Ontological Fram ew ork for Clinical Trials Managem ent

SLIDE 22

ITN Informatics Core at Stanford

The goals of our collaboration are to

Design tools to help acquire and maintain

knowledge about protocol and assay designs

Use this knowledge to drive data collection

during a trial

Implement querying methods to support

trial management, and ad hoc data analysis

SLIDE 23

Building Ontologies for ITN — Epoch

RT PCR Core Kidney Core

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

Fisher Lab RNA Processing Core

Specimen Disposal Point

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

Specimen Collection Point

SLIDE 24

Building Ontologies for ITN — Epoch

Epoch Ontologies

Protocol Model Protocol Schema Mechanistic Study Plan Assay Model Specim en Container Model Specimen Workflow Site Model Specimen Container Set Clinical Model Activity Assay Virtual Trial Data Model Visit

SLIDE 33

Knowledge-Acquisition Environment

OW L (the Web Ontology Language proposed by W3C) SW RL (the Semantic Web Rule Language) to specify constraints and queries Protégé-OW L editor to enter ontologies in OWL and SWRL

SLIDE 34

Epoch Protocol Model

SLIDE 35

Epoch Protocol Model

SLIDE 36

Schedule of Events

Visit Period Time Anchor Annotation Temporal Constraint Activity

SLIDE 37

Protocol Model – Study Schema

SLIDE 38

Study Schema

SLIDE 39

Study Schema – a Temporal Sequence

f Periods

SLIDE 40

Visit Flow – a Temporal Sequence of Visits

SLIDE 41

Visit

SLIDE 42

Visit – different Visit names

SLIDE 43

Specimen Table

Visit Time constraint as a SWRL rule

Check if the participant's visits occurred w ithin the visit tim e w indow specifications

SLIDE 74

Constraints expressed as SWRL rules

On days that both immunotherapy and omalizumab are administered, omalizumab will be injected 60 minutes after the immunotherapy.

SLIDE 75

ITN Informatics Core at Stanford

The goals of our collaboration are to

Design tools to help acquire and maintain

knowledge about protocol and assay designs

Use this knowledge to drive data collection

during a trial

Implement querying methods to support

Epoch Knowledge Base Knowledge Base Server Clinical Trial Database Model-Database Mapper

Clinical Trials Managem ent Applications

Query / Rule Engine SWRL | JESS OWL | SWRL API Utility Functions

SLIDE 82

Configuration of ImmunoTrak – the Specimen Workflow Application

SLIDE 83

ImmunoTrak Configuration File

SLIDE 84

Configuration of ImmunoTrak – the Specimen Workflow Application

Epoch Knowledge Base ImmunoTrak Configuration ImmunoTrak ― Specimen Workflow

1 2

SLIDE 85

Ontology Mapping to generate XML Document

Epoch Ontology I m m unoTrak Configuration XML

Protocol( ?p) ^ hasSitePlan( ?p, ?sp) ^ hasStudySites( ?sp, ?site) ^ hasSiteI D( ?site, ?siteI D) ^ hasParticipant( ?site, ?participants) ^ hasParticipantI Ds( ?participant, ?participantI D) ^ hasStudyI nform ation( ?sp, ?studyI nfo) ^ hasStudyI D( ?studyI nfo, ?hasStudyI D)

> XMLDocum ent( ?p) ^ hasNodeNam e( ?p, "Study") ^

XMLCom ponent( ?participant) ^ hasNodeNam e( ?participant, "Participant") ^ hasCom ponents( ?p, ?participant) ^ hasAttribute( ?participant, ?participantI D) ^ hasAttributeNam e( ?participantI D, "id">

XML Docum ent Ontology

SW RL

SLIDE 86

Protégé OWL

Clinical Ontology Generic Protocol Model Assay Ontology Site Ontology Electronic CRF Participant Visits Specimen Identification Specimen Workflow

Protocol Protocol Protocol+ Specimen Table Applications for Knowledge Specification Applications for Data Collection Applications for Clinical Trials Management CRF Tracking Core Data Repository Protocol Protocol Specific Assays Protocol Protocol Specific Sites Epoch Ontologies

Container Ontology

Protocol Protocol Specific Kits