Bridging Epoch: Mapping Two Clinical Trial Ontologies 10th - PowerPoint PPT Presentation

Bridging Epoch: Mapping Two Clinical Trial Ontologies 10th International Protégé Conference July 17, 2007 Samson W. Tu 1 , Douglas Fridsma 2 , Ravi D. Shankar 1 , Martin O'Connor 1 , Amar K. Das 1 , David B. Parrish 3 1 Stanford University, USA 2 University of Pittsburgh, USA 3 The Immune Tolerance Network, Pittsburgh, PA, USA

Problem: Ontologies and semantic interoperability Ontology 1 Ontology 2 2

BRIDG: Biomedical Research Integration Group � Part of US NCI Cancer Biomedical Informatics Grid (caBIG) � Stakeholders include US FDA, HL7, CDISC � Create shared domain model for BRIDG protocol-driven clinical research � Comprehensive � Consensus-based � Abstract and context neutral 3

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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 model EPOCH � Developed at Stanford Medical Informatics � Designed to provide semantic foundation for management of clinical trials 6

Management of clinical trials involves complex data and multiple groups CRO Core CRF Labs Assay Data Results Assay Queries Center Group Reports Protocol S cee g t D( F K ) C o d e escr D ip tio n Tubes E T L M ap in p g H ead er H L A B u sin essR u leH ead er E r n o llm en D t t eID r (F ) K C n o vN u m S tu d yGr o u p ID ( K F ) eco R d r t D K F ) M ap H d ID r B R H d r ID IsL o calL ab U ser (F ID K ) D o n r o ID M ap p in g N am e V er sio n IR B A p p r o ved lD t R ecip ien tID S o ce r u R B am N e Gen er icL o ad IT N A p p r ved o t D R eco r D d t C o e_C r n o tacts V er sio n B u d g etA p p o r ved D t t D Gen o L ad ID S cr een in g ailu F eR r esaso n ID C r o eID ( F K ) (F K ) A ctivatio n t D S cr een in g ailu F r eC o m m en t C o e_A r ssays ileN F am e C n o tactT yp eID (F ) K ileD F ir R eco r D d t U ser ID (F K ) C o eID r (F K ) E T L M ap p in g etail D H A L B u sin essR u leD etail U ser ID (F K ) U ser ID ( F K ) B R D etailID R o wN u m b er A ssayID (F K ) am p leID (F K ) M ap D tlID R eco D r d t S p ecim en T yp eID ( F K ) Group D (F K ) T ar g etT ab le o C lu m n N am e B ar co e d S o r u ceC o lu m n C ellV alu e A ccessio n eco R r d t D D(F K ) ar T g etT ab le ar T g etC o lu n m B ar co d eID F K ) R B V alu e o S r u ce ccessio A n ID U ser ID (F ) K ar T g etC o lu n m yp T e V er sio n tu S d yID (F K ) D(F K ) M ap d H r ID ar T g etC o lu m n T yp e o C eID r (F ) K Specim en Manufacturer E t d n ter ed S u b jectID (F K ) (F K ) R B d H ID r F ilen am e ileR F eq u estL ist Clinical o L ad ID isitID V ( F K ) S S M _A cc m e H A L ver E tL o g r T an sm issio n D t ar B co d e eID (F K ) T r an sactio C n o d eID (F K ) F ileR eq u estL istID H L A E ven tL o ID g o C llectio D n t n t H L A D ataIm p o tL r o g R eco d r D t R eco r d D t S tatu s S tu y_ID d d D t E ven tD esc Gen er icL o ad atch B U ser ID (F ) K F ileN am e R eco d r t D Im p o r tL o g ID GL B atch ID U ser ( ID F K ) S ite_ID D( F K ) D ecto ir r y Op er ato ID r F ileN am e C o r eS am p le_D etail R eq u estID (F K ) P ar ticip an F ileD ir V isit_N m u GL B atch ID S tu d yN u m R eco D d r t S u b ject M essag e C d o e C o r eS am leID p (F K ) C o llectio n C o fig n P ar am eter F ileN am e S b u jectID F ileR eq u est V isitN u m o C r eS am p le ar B co d eID (F K ) C o llectio n o C n fig P ar am eter ID S ecim p en yp T e QC S am p leID (F K ) S iteID (F K ) eq R u estID B ar co d e r P o cessID (F K ) P ticip ar an tID C r o eS am p leID V alid atio n C d o eID (F K ) P ar ticip an tID eq R u estD t S p ecim en Table N am e V alid atio D n t S d tu yGr o u ID p (F K ) L ab B co ar d e S tu yID d ( F ) K C o m p leted D t alu V e D escr tio ip Trial n A ccessio ID n (F K ) R eco d r D t eco R r d D t m E ailA d d r e ss S ite_D ev_ eco R d r D t R eco r D d t P o r cessin C g o d eID (F ) K U ser ID (F ) K ser U ID F ( K ) tatu S s C o r e_D ev U ser ID (F ) K Op er ato r ID S am p leT yp eID (F ) K F ileN am e O_S tu d y_ A r ch ive A ccessio n ID R ecd t D ileT F yp e O_S ite_ID K ) p r ataE tD xtr actR eq u est S am p leT yp e O_P ar tici A r ch iveID A n alysisD t M essag e r P cess o T ech am n e R eq u estN u m b er S am p leT yp eID r ch A iveID (F ) K O_V isit_N C o r eID ( F K ) F ilen am e N am e U ser N am e O_C o llec P r o cessID F ( ) K P r o cessID D tOfR eq est u O_C o llec E xter n alID D tR eq ir u ed B y R eco d r t D N am e N am e B ar co eID d 9 U ser ID (F K ) S M S _Issu es O_S p ecim D ir ecto r y R eco r D d t R eq u esto r N am e In valid ta S Kit S p ecim en T yp eID (F K ) R eq esto u r h P o n e Issu eId R eco r D d t U ser ID ( F K ) R eco d r D t In valid o C S tu yN d u m alid V atio n C o d e o C eS r am leID p ( F K ) U ser ID ( F K ) U ser ID (F K ) In valid C o C r o e V alid atio n C o d eID extM T sg In valid ID S S o u r ce o C r e_Issu es Data S tu yD d ata tatu S s C o e d In valid ID P S o u r ceID D evC o d e QC S am p les R eco r d D t Issu eID R esear ch D evelo p m en t D escr ip tio n In valid E n C o eID r (F K ) C o e r D evC o d eID R eco r d D t R eco d r D t S tar tD t er V sio n S tu d y C o d e U ser ID (F K ) D escr ip tio n E n d t D S M S _Qu Schedule o C r esam leID p D escr ip tio n V isitsD etail S tar tD t eq R u ested y B Qu y er GetC m o m en ts D ataF o r at m n E D d t escr D ip tio n R eco r d t D P o r cessin C g o d e S M S _Issu ed _Q u er ies S tu y d R eco r d t D R eq estD u t In clu d eD eviatio n C o d es Issu eID (F K ) ield F U ser ID (F ) K In clu d eT r tC o h o r t P o r cessin C g d o eID Qu er y Report U ser ID (F ) K R esp o n se Qu er y_ID (F ) K S ite_q In clu d eU n valid ated am S les p C d o e p cr esu R lt_Qu al S tatu s F ield ID S ecialIn p str u ctio n s D escr tio ip n eco R d r t D Qu er y C eS r o am p leID (F K ) o C r eS am leid p (F K ) N am e A ssig ed n T o R eco r d D t eso R lved Qu er y D escr ip tio n A ssig ed n D t U ser ID (F K ) Qu er y estID T (F ) K o S u ce_F r ield s ep R licateID R eco d r D t P lan S tatu s Qu y er o S u r ceF ield ID U ser ID (F K ) D ate_ B aseV isitID (F K ) D tP lan A vailab le T an r sp lan t S cr een in g F ailu r eR e aso n o S u r ceID F ( K ) D tP lan F al in D ate_ Qu alifier T r an sactio n C o d e C o r eS am p le_D evC o d e r T an sp lan tId S cr een in g ailu F r eR easo n ID F ield ID F ( K ) R eq estC u lo sed B y D ate_ tL A east T r an sactio C n o d eID o C eS r am leID p (F K ) ecip R ien t_S u b jectId C o d e In itiat of Events S am leQu p ality Or in d al D evC o d eID (F K ) C lo sed D t o D o n r _S u jectId b R eco r d D t C o d e S iteD etails D escr ip tio n R eso l C alib ato r r Qu ality N o es t Or an g E ab n led E xter n R eco d r D t S kip F lag D escr ip tio n In fo m r aticsN te o eco R d r t D R eco r d D t R eco r d D t R eco r d t D R ecU p d ated B y S tu yID d R eso l U ser ID (F K ) Op er ato r U ser ID (F K ) U ser ID ( K F ) ser U ID (F K ) R ecU p d ated On D ate_ S tu d yId Qu er y D ataE xtr actT yp e Cim arron Queries Operations Reports Group I m m unoTrak Tube 7 Table

Three goals of EPOCH ontologies � 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 8

EPOCH ontologies created in Protégé OWL 9