The Development of the Clinical Trial Ontology to standardize dissemination of clinical trial data. Ravi Shankar

Save this PDF as:
 WORD  PNG  TXT  JPG

Size: px
Start display at page:

Download "The Development of the Clinical Trial Ontology to standardize dissemination of clinical trial data. Ravi Shankar"

Transcription

1 The Development of the Clinical Trial Ontology to standardize dissemination of clinical trial data Ravi Shankar

2 Open access to clinical trials data advances open science Broad open access to entire clinical trial data is on the rise Tremendous opportunity to evaluate new hypotheses that were not originally formulated in the studies by performing cross analysis of clinical trials by combining with other open biomedical datasets We are developing standards-based methodologies for uniformly representing clinical trial data to support dissemination, integration and analysis.

3 Industry and Government Opening the Clinical Trial Data Vault

4 clinicalstudydatarequest.com SAS Datasets Multiple proprietary data models

5 SAS datasets EXCEL, ASCII files Multiple proprietary data models

6 immport.niaid.nih.gov MySQL dumps Proprietary data model

7 New Open Science by Integrating Open Clinical Trial Data with Biomedical Datasets Looking at data is good; reanalyzing it is great Clinical trial results can be reproduced and expanded Discover new markers for personalized medicine While individual studies are great, pooling studies may be more powerful Pooling experimental results enables new questions Let s learn why trials work and fail Integration and reanalysis requires uniform data representation and easy access to data in the analytical environments

8 Clinical Trial Data To support the integration and analysis of clinical trials data We are creating uniform representations of clinical trial data. We are enabling easy access to uniformly represented clinical trial data in analytical environments. represent Uniformly Represented Clinical Trial Data export bridge Open Clinical Trial Repositories Dissemination Analytical Environments (R, SAS) Analysis

9 The 5 Major Steps from Raw Data to to Publish to Ready-for-analysis 1. Scope the clinical trial data types that we want to include for dissemination purposes. 2. Define a set of clinical trial domain entities (an ontology) required to uniformly represent the clinical trial data. 3. Using the ontology, encode specific clinical trial data to create uniformly represented data. 4. Publish the encoded clinical trial data. 5. Create bridges between the encoded data and analytical environments to provide easy access to data for analysis.

10 Towards Minimum Information About Clinical Trial for Dissemination Study Summary Study Objectives and Outcome Measures Study Design Schedule of Activities Case Report Form Templates Study Subjects Clinical Data Experimental Data Adverse Events Analysis Data

11 Using Semantic web standards to represent and disseminate clinical trial data Semantic web standards allow data to be shared and reused over the web OWL Web Ontology Language SPARQL RDF Query Language RDF Resource Description Framework URI Uniform Resource Identifier

12 Classes (OWL ontology) Instances (RDF triples) CDISC 2013

13 Building a Standards-Based Clinical Trial Ontology a Formal Description of the Clinical Trial Domain Leverage of data elements defined in CDISC Standards e.g. Study, Arm, Study Subject Link with appropriate reference biomedical ontologies Clinical Trial Ontology (CTO) PRM TDM CDASH SDTM Data Dissemination Elements ODM ADaM SEND BRIDG NCI Thesaurus SNOMED CT Use Upper-level, Structural and Domain Ontologies BFO RDF Data Cube GO NDF-RT BAO PRO CL IAO OGMS

14 CDISC Foundational Standards PRM (Protocol Representation Model) Study objectives, methods, organization,... CDASH (Clinical Data Acquisition Standards Harmonization) Content standards for case report forms LAB (Lab Data Model) Interchange of laboratory data between labs and CROs SDTM (Study Data Tabulation Model) Structure for data submission to regulatory agencies ADaM (Analysis Data Model) SDTM complement to detail statistical analysis CDISC

15 A list of terms from CDISC PRM and SDTM standards

16 Basic Formal Ontology (BFO) CDISC

17 independent continuant organism dependent continuant quality temperature occurrent process process profile course of temperature changes John John s temperature John s temperature history CDISC 2013

18 Building down the Clinical Trial Ontology participates in CDISC

19 Describing the Clinical Trial Domain as a Set of OWL Axioms Descriptions of a clinical trial entity such as its parent entity, its relationships with other entities and value restrictions are formally expressed as logical axioms to create the Clinical Trial Ontology InterventionalStudy is a subtype of Study Study has title that is of type string is divided into relates Study to an Arm Study Subject is a subtype of Person with role as Subject Role

20 Representing Clinical Trial Data as a Collection of RDF Triples In RDF, data is represented as triples predicate Subject Object arm1 Using the entities in the CTO ontology (Study, title, is divided into, Planned Activity, etc.), the entire CCTPT_SW01 data can be represented as a collection of RDF triples title CCTPT_SW01 type of type of Arm Study CCTPT_SW01 CCTPT_SW01 Is divided into arm1 A double-blind randomized trial of steroid withdrawal label... arm1 Steroid withdrawal arm

21 Examples of Temporal Constraints in Clinical Trials Plan Participant is ineligible if he/she had vaccination with a live virus within the last 6 weeks before enrollment Visit 17 must occur at least 1 week but no later than 4 weeks after the end of 2003 ragweed season Screening visit evaluations must occur between 30 days prior to Visit -1 and 45 days prior to Visit 0 Monitor cyclosporine levels 3 times per week while in-patient, then weekly as out-patient CDISC 2013

22 Constraint Expression Ontology CDISC

23 Anchored Duration - A temporal constraint expression

24 The Anchored Duration class is used to specify relative start time of a visit Time Axis Visit 0 time 2 weeks ± 3days Visit 1 start time

25 Multi-dimensional clinical data CDISC

26 Exploring RDF Data Cube for representing and analyzing multi-dimensional longitudinal data CUBE - a set of observations indexed by dimensions (e.g., subjects, months after transplant ) describing measures (e.g., standard height) interpreted according to attributes (e.g., z-score) OBSERVATION measured values (with attributes) at dimensions SLICE optional grouping of observations by fixing dimensions

27 RDF Data Cube Vocabulary Based on Statistical Data and Metadata Exchange (SDMX) 2.0 Information Model CDISC

28 The RDF Data Cube can be sliced and diced to analyze clinical data

29 Building the Clinical Trial Ontology in Protege CDISC

30 Representing Clinical Trial Data as a Collection of RDF Triples In RDF, data is represented as triples predicate Subject Object arm1 Using the entities in the CTO ontology (Study, title, is divided into, Planned Activity, etc.), the entire CCTPT_SW01 data can be represented as a collection of RDF triples title CCTPT_SW01 type of type of Arm Study CCTPT_SW01 CCTPT_SW01 Is divided into arm1 A double-blind randomized trial of steroid withdrawal label... arm1 Steroid withdrawal arm

31 Named RDF Graphs The collection of RDF triples can be viewed as a graph CCTPT_SW01_Graph type of Arm Study arm1 type of is divided into title CCTPT_SW01 label Steroid withdrawal arm A double-blind randomized trial of steroid withdrawal

32 Storing the RDF Encoded Data using 4store, an RDF database Clinical Trial Data represent Clinical Trial Ontology (OWL) OWL / RDF Editor Encoded Clinical Trials (RDF) 4store CDISC Standards, Other Ontologies & Linked Data export bridge Open Clinical Trial Repositories Dissemination Analytical Environments (R, SAS) Analysis

33 Querying 4store for Clinical Trial Data using SPARQL Clinical Trial Data represent Clinical Trial Ontology (OWL) OWL / RDF Editor Encoded Clinical Trials (RDF) 4store CDISC Standards, Other Ontologies & Linked Data export Jena RDF API bridge rrdf Open Clinical Trial Repositories Dissemination Clinical Trial Data Objects in R Analysis

34 Loading the RDF Encoded Clinical Trial Data in R a prototype bridge Create R data classes that correspond to the Clinical Trial Ontology (CTO) entities. CTO Entities Study title (string) R Classes Study <- setrefclass("study", fields = list(title = "character )) Query the RDF triples and populate the R classes with clinical trial data. Using R RDF libraries for SPARQL queries CDISC 2013

35 > cctpt_sw01 = loadstudy(<clinical Trial URI>) A single line of R code can load the entire clinical trial data into R for analysis > cctpt_sw01 = loadstudy(" > cctpt_sw01$title title "A DOUBLE-BLIND RANDOMIZED TRIAL OF STEROID WITHDRAWAL IN SIROLIMUS- AND CYCLOSPORINE-TREATED PRIMARY TRANSPLANT RECIPIENTS" > cctpt_sw01$arms [[1]] Reference class object of class "Arm" Field "name": name "Control arm" [[2]] Reference class object of class "Arm" Field "name": name "Steroid withdrawal arm" CDISC 2013

36 CDISC Standards CDISC

37 CDISC Terminologies NCI EVS CDISC

38 CDISC

39 CDISC

40 CDISC

41 CDISC SHARE an electronic library of standards CDISC

42 CDISC

43 CDISC

44 CDISC

45 CDISC

46 CDISC2RDF AstraZeneca, Roche FDA/PhUSE Emerging Technologies / Semantic Technology Draft representations: CDISC

USE CDISC SDTM AS A DATA MIDDLE-TIER TO STREAMLINE YOUR SAS INFRASTRUCTURE

USE CDISC SDTM AS A DATA MIDDLE-TIER TO STREAMLINE YOUR SAS INFRASTRUCTURE USE CDISC SDTM AS A DATA MIDDLE-TIER TO STREAMLINE YOUR SAS INFRASTRUCTURE Kalyani Chilukuri, Clinovo, Sunnyvale CA WUSS 2011 Annual Conference October 2011 TABLE OF CONTENTS 1. ABSTRACT... 3 2. INTRODUCTION...

More information

Pilot. Pathway into the Future for. Delivery. April 2010 Bron W. Kisler, CDISC Senior Director bkisler@cdisc.org

Pilot. Pathway into the Future for. Delivery. April 2010 Bron W. Kisler, CDISC Senior Director bkisler@cdisc.org SHARE S&V Document and the Pilot Pathway into the Future for Standards Development and Delivery April 2010 Bron W. Kisler, CDISC Senior Director bkisler@cdisc.org 1 CDISC Mission To develop and support

More information

BRIDGing CDASH to SAS: How Harmonizing Clinical Trial and Healthcare Standards May Impact SAS Users Clinton W. Brownley, Cupertino, CA

BRIDGing CDASH to SAS: How Harmonizing Clinical Trial and Healthcare Standards May Impact SAS Users Clinton W. Brownley, Cupertino, CA BRIDGing CDASH to SAS: How Harmonizing Clinical Trial and Healthcare Standards May Impact SAS Users Clinton W. Brownley, Cupertino, CA ABSTRACT The Clinical Data Interchange Standards Consortium (CDISC),

More information

Electronic Submission of Regulatory Information, and Creating an Electronic Platform for Enhanced Information Management

Electronic Submission of Regulatory Information, and Creating an Electronic Platform for Enhanced Information Management Written Notice of Participation by the Clinical Data Interchange Standards Consortium (CDISC) and Written Statement for Discussion Topics to be Addressed In the FDA Public Hearing: Electronic Submission

More information

Large Scale Healthcare Data Integration using the Semantic Web

Large Scale Healthcare Data Integration using the Semantic Web Large Scale Healthcare Data Integration using the Semantic Web John T.E. Timm (presenter) Ariel Farkash Sondra R. Renly Oral Presentation at MIE 2011 August 30 th, 2011 Oslo, Norway Objectives Create a

More information

UTILIZING CDISC STANDARDS TO DRIVE EFFICIENCIES WITH OPENCLINICA Mark Wheeldon CEO, Formedix Boston June 21, 2013

UTILIZING CDISC STANDARDS TO DRIVE EFFICIENCIES WITH OPENCLINICA Mark Wheeldon CEO, Formedix Boston June 21, 2013 UTILIZING CDISC STANDARDS TO DRIVE EFFICIENCIES WITH OPENCLINICA Mark Wheeldon CEO, Formedix Boston June 21, 2013 AGENDA Introduction Real World Uses : Saving Time & Money. Your Clinical Trials Automated.

More information

CDISC Roadmap Outline: Further development and convergence of SDTM, ODM & Co

CDISC Roadmap Outline: Further development and convergence of SDTM, ODM & Co CDISC Roadmap Outline: Further development and convergence of SDTM, ODM & Co CDISC Ausblick: Weitere Entwicklung und Konvergenz der CDISC-Standards SDTM, ODM & Co. Jozef Aerts - XML4Pharma Disclaimer Views

More information

4. Executive Summary of Part 1 FDA Overview of Current Environment

4. Executive Summary of Part 1 FDA Overview of Current Environment Public Meeting Regulatory New Drug Review: Solutions for Study Data Exchange Standards 1. Background Meeting Summary Food and Drug Administration White Oak, MD November 5, 2012 10am 4pm On November 5,

More information

Business & Decision Life Sciences What s new in ADaM

Business & Decision Life Sciences What s new in ADaM Business & Decision Life Sciences What s new in ADaM Gavin Winpenny 23 rd June 2015 Agenda What s happening CDISC and Regulatory Submission Landscape ADaM Implementation Guide ADaM Data Structures for

More information

Rationale and vision for E2E data standards: the need for a MDR

Rationale and vision for E2E data standards: the need for a MDR E2E data standards, the need for a new generation of metadata repositories Isabelle de Zegher, PAREXEL Informatics, Belgium Alan Cantrell, PAREXEL, United Kingdom Julie James, PAREXEL Informatics, United

More information

Bringing Order to Your Clinical Data Making it Manageable and Meaningful

Bringing Order to Your Clinical Data Making it Manageable and Meaningful CLINICAL DATA MANAGEMENT Bringing Order to Your Clinical Data Making it Manageable and Meaningful eclinicalsol.com DATA IS SIMPLY BEAUTIFUL DATA STACKS IN STANDARD FORMATION This imaginative visual suggests

More information

Programme Guide PGDCDM

Programme Guide PGDCDM Post Graduate Diploma in Clinical Data Management and Biostatistics with SAS Programme Guide PGDCDM School of Health Sciences Indira Gandhi National Open University WHY THIS PROGRAMME? The Post Graduate

More information

Statistical Operations: The Other Half of Good Statistical Practice

Statistical Operations: The Other Half of Good Statistical Practice Integrating science, technology and experienced implementation Statistical Operations: The Other Half of Good Statistical Practice Alan Hopkins, Ph.D. Theravance, Inc. Presented at FDA/Industry Statistics

More information

Telling the Data Story: Use of Informatics, Harmonized Semantics and Metadata in the National Children s Study

Telling the Data Story: Use of Informatics, Harmonized Semantics and Metadata in the National Children s Study Telling the Data Story: Use of Informatics, Harmonized Semantics and Metadata in the National Children s Study John Lumpkin, MS, MBA, PMP Steven Hirschfeld, MD, PhD NIH-NICHD-National Children s Study

More information

PhUSE Annual Meeting, London 2014

PhUSE Annual Meeting, London 2014 PhUSE Annual Meeting, London 2014 Metadata, Study data standards, Master data, terminology, interoperability: Key concepts underlying compliance to FDA guidance on electronic submission Isabelle de Zegher,

More information

Introduction to the CDISC Standards

Introduction to the CDISC Standards Introduction to the CDISC Standards Sandra Minjoe, Accenture Life Sciences, Wayne, Pennsylvania ABSTRACT The Clinical Data Interchange Standards Consortium (CDISC) encompasses a suite of standards across

More information

Automate Data Integration Processes for Pharmaceutical Data Warehouse

Automate Data Integration Processes for Pharmaceutical Data Warehouse Paper AD01 Automate Data Integration Processes for Pharmaceutical Data Warehouse Sandy Lei, Johnson & Johnson Pharmaceutical Research and Development, L.L.C, Titusville, NJ Kwang-Shi Shu, Johnson & Johnson

More information

Semantic Interoperability

Semantic Interoperability Ivan Herman Semantic Interoperability Olle Olsson Swedish W3C Office Swedish Institute of Computer Science (SICS) Stockholm Apr 27 2011 (2) Background Stockholm Apr 27, 2011 (2) Trends: from

More information

An Ontology-based Architecture for Integration of Clinical Trials Management Applications

An Ontology-based Architecture for Integration of Clinical Trials Management Applications An Ontology-based Architecture for Integration of Clinical Trials Management Applications Ravi D. Shankar, MS 1, Susana B. Martins, MD, MSc 1, Martin O Connor, MSc 1, David B. Parrish, MS 2, Amar K. Das,

More information

CDISC Journal. The BRIDG Model and a Model Implementation: The Clinical Trial Registration and Results HL7 Message

CDISC Journal. The BRIDG Model and a Model Implementation: The Clinical Trial Registration and Results HL7 Message CDISC Journal Clinical Data Interchange Standards Consortium O ctober 2011 The BRIDG Model and a Model Implementation: The Clinical Trial Registration and Results HL7 Message By Julie Evans and Abdul-Malik

More information

WHITE PAPER. CONVERTING SDTM DATA TO ADaM DATA AND CREATING SUBMISSION READY SAFETY TABLES AND LISTINGS. SUCCESSFUL TRIALS THROUGH PROVEN SOLUTIONS

WHITE PAPER. CONVERTING SDTM DATA TO ADaM DATA AND CREATING SUBMISSION READY SAFETY TABLES AND LISTINGS. SUCCESSFUL TRIALS THROUGH PROVEN SOLUTIONS WHITE PAPER CONVERTING SDTM DATA TO ADaM DATA AND CREATING SUBMISSION READY SAFETY TABLES AND LISTINGS. An innovative approach to deliver statistical analysis and data in a CDISC ADaM complient manner

More information

Implementation of SDTM in a pharma company with complete outsourcing strategy. Annamaria Muraro Helsinn Healthcare Lugano, Switzerland

Implementation of SDTM in a pharma company with complete outsourcing strategy. Annamaria Muraro Helsinn Healthcare Lugano, Switzerland Italian-Speaking CDISC User Group 2008 Implementation of SDTM in a pharma company with complete outsourcing strategy Annamaria Muraro Helsinn Healthcare Lugano, Switzerland Background Full outsourcing

More information

Business & Decision Life Sciences CDISC Workshop: From SDTM to ADaM: Mapping Methodologies

Business & Decision Life Sciences CDISC Workshop: From SDTM to ADaM: Mapping Methodologies Business & Decision Life Sciences CDISC Workshop: From SDTM to ADaM: Mapping Methodologies Jessica Minkue Mi Edou / 18th September 2014 From SDTM to ADaM: Mapping Methodologies CDISC and ADaM Introduc0on

More information

Managing and Integrating Clinical Trial Data: A Challenge for Pharma and their CRO Partners

Managing and Integrating Clinical Trial Data: A Challenge for Pharma and their CRO Partners Managing and Integrating Clinical Trial Data: A Challenge for Pharma and their CRO Partners Within the Pharmaceutical Industry, nothing is more fundamental to business success than bringing drugs and medical

More information

A Brief Introduc/on to CDISC SDTM and Data Mapping

A Brief Introduc/on to CDISC SDTM and Data Mapping A Brief Introduc/on to CDISC SDTM and Data Mapping Agenda Flow of Clinical Trials Data The Problem Introducing CDISC Understanding SDTM Concepts of Data Mapping References 5/3/10 2 Flow of Clinical Trials

More information

How semantic technology can help you do more with production data. Doing more with production data

How semantic technology can help you do more with production data. Doing more with production data How semantic technology can help you do more with production data Doing more with production data EPIM and Digital Energy Journal 2013-04-18 David Price, TopQuadrant London, UK dprice at topquadrant dot

More information

Semantics and Ontology of Logistic Cloud Services*

Semantics and Ontology of Logistic Cloud Services* Semantics and Ontology of Logistic Cloud s* Dr. Sudhir Agarwal Karlsruhe Institute of Technology (KIT), Germany * Joint work with Julia Hoxha, Andreas Scheuermann, Jörg Leukel Usage Tasks Query Execution

More information

How to build ADaM from SDTM: A real case study

How to build ADaM from SDTM: A real case study PharmaSUG2010 - Paper CD06 How to build ADaM from SDTM: A real case study JIAN HUA (DANIEL) HUANG, FOREST LABORATORIES, NJ ABSTRACT: Building analysis data based on the ADaM model is highly recommended

More information

Package R4CDISC. September 5, 2015

Package R4CDISC. September 5, 2015 Type Package Title Read CDISC Data Files Version 0.4 Date 2015-9-5 Depends R (>= 3.0.3, XML Author Package R4CDISC September 5, 2015 Maintainer URL https://github.com/i-akiya/r4cdisc

More information

CDISC and Clinical Research Standards in the LHS

CDISC and Clinical Research Standards in the LHS CDISC and Clinical Research Standards in the LHS Learning Health System in Europe 24 September 2015, Brussels Rebecca D. Kush, PhD, President and CEO, CDISC CDISC 2015 1 CDISC Healthcare Link Goal: Optimize

More information

Linked Statistical Data Analysis

Linked Statistical Data Analysis Linked Statistical Data Analysis Sarven Capadisli 1, Sören Auer 2, Reinhard Riedl 3 1 Universität Leipzig, Institut für Informatik, AKSW, Leipzig, Germany, 2 University of Bonn and Fraunhofer IAIS, Bonn,

More information

«How we did it» Implementing CDISC LAB, ODM and SDTM in a Clinical Data Capture and Management System:

«How we did it» Implementing CDISC LAB, ODM and SDTM in a Clinical Data Capture and Management System: Implementing CDISC LAB, ODM and SDTM in a Clinical Data Capture and Management System: «How we did it» 27 April 2006 Berlin CDISC Interchange Xavier Bessette, [i-clinics] Jozef Aerts, XML4Pharma Who are

More information

SDTM AND ADaM: HANDS-ON SOLUTIONS

SDTM AND ADaM: HANDS-ON SOLUTIONS SDTM AND ADaM: HANDS-ON SOLUTIONS CDISC French Speaking User Group Paris, France 17 February 2012 Joris De Bondt, Head Data Standards & Process Improvements Tineke Callant, Senior Biostatistical Analyst

More information

End-to-End E-Clinical Coverage with Oracle Health Sciences InForm GTM

End-to-End E-Clinical Coverage with Oracle Health Sciences InForm GTM End-to-End E-Clinical Coverage with InForm GTM A Complete Solution for Global Clinical Trials The broad market acceptance of electronic data capture (EDC) technology, coupled with an industry moving toward

More information

Addressing Self-Management in Cloud Platforms: a Semantic Sensor Web Approach

Addressing Self-Management in Cloud Platforms: a Semantic Sensor Web Approach Addressing Self-Management in Cloud Platforms: a Semantic Sensor Web Approach Rustem Dautov Iraklis Paraskakis Dimitrios Kourtesis South-East European Research Centre International Faculty, The University

More information

AgroPortal. a proposition for ontologybased services in the agronomic domain

AgroPortal. a proposition for ontologybased services in the agronomic domain AgroPortal a proposition for ontologybased services in the agronomic domain Clément Jonquet, Esther Dzalé-Yeumo, Elizabeth Arnaud, Pierre Larmande Why ontologies? Why an ontology repository? 2 Biologist

More information

Paper DM10 SAS & Clinical Data Repository Karthikeyan Chidambaram

Paper DM10 SAS & Clinical Data Repository Karthikeyan Chidambaram Paper DM10 SAS & Clinical Data Repository Karthikeyan Chidambaram Cognizant Technology Solutions, Newbury Park, CA Clinical Data Repository (CDR) Drug development lifecycle consumes a lot of time, money

More information

Use of Electronic Health Records in Clinical Research: Core Research Data Element Exchange Detailed Use Case April 23 rd, 2009

Use of Electronic Health Records in Clinical Research: Core Research Data Element Exchange Detailed Use Case April 23 rd, 2009 Use of Electronic Health Records in Clinical Research: Core Research Data Element Exchange Detailed Use Case April 23 rd, 2009 Table of Contents 1.0 Preface...4 2.0 Introduction and Scope...6 3.0 Use Case

More information

Semantic Modeling with RDF. DBTech ExtWorkshop on Database Modeling and Semantic Modeling Lili Aunimo

Semantic Modeling with RDF. DBTech ExtWorkshop on Database Modeling and Semantic Modeling Lili Aunimo DBTech ExtWorkshop on Database Modeling and Semantic Modeling Lili Aunimo Expected Outcomes You will learn: Basic concepts related to ontologies Semantic model Semantic web Basic features of RDF and RDF

More information

ADaM or SDTM? A Comparison of Pooling Strategies for Integrated Analyses in the Age of CDISC

ADaM or SDTM? A Comparison of Pooling Strategies for Integrated Analyses in the Age of CDISC Paper CD01 ADaM or SDTM? A Comparison of Pooling Strategies for Integrated Analyses in the Age of CDISC Joerg Guettner, Bayer Pharma AG, Wuppertal, Germany Alexandru Cuza, UCB Biosciences GmbH, Monheim,

More information

Using SAS in Clinical Research. Greg Nelson, ThotWave Technologies, LLC.

Using SAS in Clinical Research. Greg Nelson, ThotWave Technologies, LLC. Using SAS in Clinical Research Greg Nelson, ThotWave Technologies, LLC. Outline Introduction and Overview SAS 30 years of evolution The SAS 9 Platform Clinical Research Imperatives Summary and Conclusions

More information

EFFECTIVE AND OPERATIONAL USE OF CDISC STANDARDS & STUDY METADATA THROUGH SAS LIFE SCIENCE ANALYTICS FRAMEWORK

EFFECTIVE AND OPERATIONAL USE OF CDISC STANDARDS & STUDY METADATA THROUGH SAS LIFE SCIENCE ANALYTICS FRAMEWORK EFFECTIVE AND OPERATIONAL USE OF CDISC STANDARDS & STUDY METADATA THROUGH SAS LIFE SCIENCE ANALYTICS FRAMEWORK - PHUSE SDE (MAY2016) STIJN ROGIERS, SENIOR INDUSTRY CONSULTANT, HEALTH & LIFE SCIENCES (GLOBAL

More information

Copyright 2012, SAS Institute Inc. All rights reserved. VISUALIZATION OF STANDARD TLFS FOR CLINICAL TRIAL DATA ANALYSIS

Copyright 2012, SAS Institute Inc. All rights reserved. VISUALIZATION OF STANDARD TLFS FOR CLINICAL TRIAL DATA ANALYSIS VISUALIZATION OF STANDARD TLFS FOR CLINICAL TRIAL DATA ANALYSIS WENJUN BAO AND JASON CHEN JMP, SAS INC. PHUSE, SHANGHAI, NOV 28, 2014 OUTLINES: CDISC Standard SDTM ADaM Interactive Standardized TLFs Tables

More information

Implementing the CDISC standards into an existing CDMS

Implementing the CDISC standards into an existing CDMS Implementing the CDISC standards into an existing CDMS Presented by Ueng-Cheng Yang (yang@ym.edu.tw) Institute of Biomedical Informatics National Yang-Ming University 1 TCT is a resource center to support

More information

PK IN DRUG DEVELOPMENT. CDISC management of PK data. Matteo Rossini Milan, 9 February 2010

PK IN DRUG DEVELOPMENT. CDISC management of PK data. Matteo Rossini Milan, 9 February 2010 Matteo Rossini Milan, 9 February 2010 Introduction to CDISC CDISC: Clinical Data Interchange Standards Consortium CDISC is a global, open, multidisciplinary, non-profit organization that has established

More information

Understanding CDISC Basics

Understanding CDISC Basics Trends in Bio/Pharmaceutical Industry Understanding CDISC Basics Jane Ma Abstract Data standards can make data and its associated program more portable. The CDISC (Clinical Data Interchange Standards Consortium)

More information

A GENERALIZED APPROACH TO CONTENT CREATION USING KNOWLEDGE BASE SYSTEMS

A GENERALIZED APPROACH TO CONTENT CREATION USING KNOWLEDGE BASE SYSTEMS A GENERALIZED APPROACH TO CONTENT CREATION USING KNOWLEDGE BASE SYSTEMS By K S Chudamani and H C Nagarathna JRD Tata Memorial Library IISc, Bangalore-12 ABSTRACT: Library and information Institutions and

More information

ABSTRACT INTRODUCTION THE MAPPING FILE GENERAL INFORMATION

ABSTRACT INTRODUCTION THE MAPPING FILE GENERAL INFORMATION An Excel Framework to Convert Clinical Data to CDISC SDTM Leveraging SAS Technology Ale Gicqueau, Clinovo, Sunnyvale, CA Marc Desgrousilliers, Clinovo, Sunnyvale, CA ABSTRACT CDISC SDTM data is the standard

More information

Did you know? Accenture can deliver business outcome-focused results for your life sciences research & development organization like these:

Did you know? Accenture can deliver business outcome-focused results for your life sciences research & development organization like these: How can Accenture Accelerated R&D BPO Services help you achieve greater business value? Did you know? Accenture can deliver business outcome-focused results for your life sciences research & development

More information

PharmaSUG2010 HW06. Insights into ADaM. Matthew Becker, PharmaNet, Cary, NC, United States

PharmaSUG2010 HW06. Insights into ADaM. Matthew Becker, PharmaNet, Cary, NC, United States PharmaSUG2010 HW06 Insights into ADaM Matthew Becker, PharmaNet, Cary, NC, United States ABSTRACT ADaM (Analysis Dataset Model) is meant to describe the data attributes such as structure, content, and

More information

PharmaSUG 2016 Paper IB10

PharmaSUG 2016 Paper IB10 ABSTRACT PharmaSUG 2016 Paper IB10 Moving from Data Collection to Data Visualization and Analytics: Leveraging CDISC SDTM Standards to Support Data Marts Steve Kirby, JD, MS, Chiltern, King of Prussia,

More information

CDISC Strategy Document Version 9 (Final BOD Approved Version) 4 December 2006

CDISC Strategy Document Version 9 (Final BOD Approved Version) 4 December 2006 CDISC Strategy Document Version 9 (Final BOD Approved Version) 4 December 2006 Introduction The Clinical Data Interchange Standards Consortium (CDISC) has established standards to support the acquisition,

More information

SDTM, ADaM and define.xml with OpenCDISC Matt Becker, PharmaNet/i3, Cary, NC

SDTM, ADaM and define.xml with OpenCDISC Matt Becker, PharmaNet/i3, Cary, NC PharmaSUG 2012 - Paper HW07 SDTM, ADaM and define.xml with OpenCDISC Matt Becker, PharmaNet/i3, Cary, NC ABSTRACT Standards are an ongoing focus of the health care and life science industry. Common terms

More information

Using SAS Data Integration Studio to Convert Clinical Trials Data to the CDISC SDTM Standard Barry R. Cohen, Octagon Research Solutions, Wayne, PA

Using SAS Data Integration Studio to Convert Clinical Trials Data to the CDISC SDTM Standard Barry R. Cohen, Octagon Research Solutions, Wayne, PA Using SAS Data Integration Studio to Convert Clinical Trials Data to the CDISC SDTM Standard Barry R. Cohen, Octagon Research Solutions, Wayne, PA ABSTRACT A new industry standard for clinical trials data,

More information

Use of Metadata to Automate Data Flow and Reporting. Gregory Steffens Novartis PhUSE 13 June 2012

Use of Metadata to Automate Data Flow and Reporting. Gregory Steffens Novartis PhUSE 13 June 2012 Use of Metadata to Automate Data Flow and Reporting Gregory Steffens Novartis PhUSE 13 June 2012 Stages of Metadata Evolution I In the beginning... No corporate or industry level data or reporting standards

More information

Einführung in die CDISC Standards CDISC Standards around the World. Bron Kisler (CDISC) & Andrea Rauch DVMD Tagung 11.-14.

Einführung in die CDISC Standards CDISC Standards around the World. Bron Kisler (CDISC) & Andrea Rauch DVMD Tagung 11.-14. Einführung in die CDISC Standards CDISC Standards around the World Bron Kisler (CDISC) & Andrea Rauch DVMD Tagung 11.-14. März 2015 1 Outline Overview of CDISC Therapeutic Area Standards SHARE Metadata

More information

Performance Analysis, Data Sharing, Tools Integration: New Approach based on Ontology

Performance Analysis, Data Sharing, Tools Integration: New Approach based on Ontology Performance Analysis, Data Sharing, Tools Integration: New Approach based on Ontology Hong-Linh Truong Institute for Software Science, University of Vienna, Austria truong@par.univie.ac.at Thomas Fahringer

More information

Classifying Adverse Events From Clinical Trials

Classifying Adverse Events From Clinical Trials Classifying Adverse Events From Clinical Trials Bernard LaSalle, Richard Bradshaw University of Utah, Biomedical Informatics, Salt Lake City, UT USA bernie.lasalle@hsc.utah.edu Abstract The use of adverse

More information

An Application Ontology to Support the Access to Data of Medical Doctors and Health Facilities in Brazilian Municipalities

An Application Ontology to Support the Access to Data of Medical Doctors and Health Facilities in Brazilian Municipalities An Application Ontology to Support the Access to Data of Medical Doctors and Health Facilities in Brazilian Municipalities Aline da Cruz R. Souza, Adriana P. de Medeiros, Carlos Bazilio Martins Department

More information

Lessons on the Metadata Approach. Dave Iberson- Hurst 9 th April 2014 CDISC Euro Interchange 2014

Lessons on the Metadata Approach. Dave Iberson- Hurst 9 th April 2014 CDISC Euro Interchange 2014 1 Lessons on the Metadata Approach Dave Iberson- Hurst 9 th April 2014 CDISC Euro Interchange 2014 2 Experience Human beings, who are almost unique in having the ability to learn from the experience of

More information

Use of standards: can we really be analysis ready?

Use of standards: can we really be analysis ready? Standards in analysis & reporting Use of standards: can we really be analysis ready? Analysis ready? Why? Reducing time to market/approval Reducing time to delivery Reducing re work Designing subsequent

More information

Data Standards and the National Cardiovascular Research Infrastructure (NCRI)

Data Standards and the National Cardiovascular Research Infrastructure (NCRI) Data Standards and the National Cardiovascular Research Infrastructure (NCRI) A partnership with Duke Clinical Research Institute (DCRI) and the American College of Cardiology Foundation (ACCF) November

More information

Dude, where s my graph? RDF Data Cubes for Clinical Trials Data.

Dude, where s my graph? RDF Data Cubes for Clinical Trials Data. Paper TT07 Dude, where s my graph? RDF Data Cubes for Clinical Trials Data. Marc Andersen, StatGroup ApS, Denmark Tim Williams, UCB BioSciences Inc, USA ABSTRACT The concept of Linked Data conjures images

More information

CREATING AND APPLYING KNOWLEDGE IN ELECTRONIC HEALTH RECORD SYSTEMS. Prof Brendan Delaney, King s College London

CREATING AND APPLYING KNOWLEDGE IN ELECTRONIC HEALTH RECORD SYSTEMS. Prof Brendan Delaney, King s College London CREATING AND APPLYING KNOWLEDGE IN ELECTRONIC HEALTH RECORD SYSTEMS Prof Brendan Delaney, King s College London www.transformproject.eu 7.5M European Commission March 2010-May 2015 Funded under the Patient

More information

End-to-End Management of Clinical Trials Data

End-to-End Management of Clinical Trials Data End-to-End Management of Clinical Trials Data A Revolutionary Step Toward Supporting Clinical Trials Analysis Over the Next Decades of Clinical Research WHITE PAPER SAS White Paper Table of Contents Introduction....

More information

SAS CLINICAL TRAINING

SAS CLINICAL TRAINING SAS CLINICAL TRAINING Presented By 3S Business Corporation Inc www.3sbc.com Call us at : 281-823-9222 Mail us at : info@3sbc.com Table of Contents S.No TOPICS 1 Introduction to Clinical Trials 2 Introduction

More information

ABSTRACT INTRODUCTION PATIENT PROFILES SESUG 2012. Paper PH-07

ABSTRACT INTRODUCTION PATIENT PROFILES SESUG 2012. Paper PH-07 Paper PH-07 Developing a Complete Picture of Patient Safety in Clinical Trials Richard C. Zink, JMP Life Sciences, SAS Institute, Cary, NC, United States Russell D. Wolfinger, JMP Life Sciences, SAS Institute,

More information

SAS Drug Development User Connections Conference 23-24Jan08

SAS Drug Development User Connections Conference 23-24Jan08 SAS Drug Development User Connections Conference 23-24Jan08 Bernd Doetzkies David Ramage Daiichi Sankyo Pharma Development DSPD Clinical Data Repository System Business Drivers System Overview People and

More information

John S. McIlwain. Data Standards Harmonization Dieter Spannknebel/Getty images

John S. McIlwain. Data Standards Harmonization Dieter Spannknebel/Getty images Volume 19, Number 5 May 2010 Your Peer-R eviewed Guide to Globa l Clinica l T ria l s M a nagement appliedclinicaltrialsonline.com Data Integration John S. McIlwain Data Standards Harmonization Dieter

More information

Open Ontology Repository Initiative

Open Ontology Repository Initiative Open Ontology Repository Initiative Frank Olken Lawrence Berkeley National Laboratory National Science Foundation folken@nsf.gov presented to CENDI/NKOS Workshop World Bank Sept. 11, 2008 Version 6.0 DISCLAIMER

More information

Bootstrapping Adoption of a Universal Exchange Language for Health Information Exchange

Bootstrapping Adoption of a Universal Exchange Language for Health Information Exchange Bootstrapping Adoption of a Universal Exchange Language for Health Information Exchange Speakers: Tajh L. Taylor, Lowell Vizenor OMG SOA in Healthcare Conference July 15, 2011 Agenda The Health Information

More information

Open Data Integration Using SPARQL and SPIN

Open Data Integration Using SPARQL and SPIN Open Data Integration Using SPARQL and SPIN A Case Study for the Tourism Domain Antonino Lo Bue, Alberto Machi ICAR-CNR Sezione di Palermo, Italy Research funded by Italian PON SmartCities Dicet-InMoto-Orchestra

More information

Overview of CDISC Implementation at PMDA. Yuki Ando Senior Scientist for Biostatistics Pharmaceuticals and Medical Devices Agency (PMDA)

Overview of CDISC Implementation at PMDA. Yuki Ando Senior Scientist for Biostatistics Pharmaceuticals and Medical Devices Agency (PMDA) Overview of CDISC Implementation at PMDA Yuki Ando Senior Scientist for Biostatistics Pharmaceuticals and Medical Devices Agency (PMDA) CDISC 2012 Outline Introduction Update of PMDA activity CDISC implementation

More information

Training/Internship Brochure Advanced Clinical SAS Programming Full Time 6 months Program

Training/Internship Brochure Advanced Clinical SAS Programming Full Time 6 months Program Training/Internship Brochure Advanced Clinical SAS Programming Full Time 6 months Program Domain Clinical Data Sciences Private Limited 8-2-611/1/2, Road No 11, Banjara Hills, Hyderabad Andhra Pradesh

More information

Transforming CliniCal Trials: The ability to aggregate and Visualize Data Efficiently to make impactful Decisions

Transforming CliniCal Trials: The ability to aggregate and Visualize Data Efficiently to make impactful Decisions : The ability to aggregate and Visualize Data Efficiently to make impactful Decisions www.eclinicalsol.com White Paper Table of Contents Maximizing Your EDC Investment... 3 Emerging Trends in Data Collection...

More information

Data modelling methods in clinical trials: Experiences from the CTMND project (ctmnd.org)

Data modelling methods in clinical trials: Experiences from the CTMND project (ctmnd.org) Data modelling methods in clinical trials: Experiences from the CTMND project (ctmnd.org) Athanasios Anastasiou, Emmanuel Ifeachor, John Zajicek & the CTMND Consortium University of Plymouth Peninsula

More information

Extracting the value of Standards: The Role of CDISC in a Pharmaceutical Research Strategy. Frank W. Rockhold, PhD* and Simon Bishop**

Extracting the value of Standards: The Role of CDISC in a Pharmaceutical Research Strategy. Frank W. Rockhold, PhD* and Simon Bishop** Extracting the value of Standards: The Role of CDISC in a Pharmaceutical Research Strategy Frank W. Rockhold, PhD* and Simon Bishop** GlaxoSmithKline Research and Development. RTP NC and Stevenage, UK

More information

Building and Customizing a CDISC Compliance and Data Quality Application Wayne Zhong, Accretion Softworks, Chester Springs, PA

Building and Customizing a CDISC Compliance and Data Quality Application Wayne Zhong, Accretion Softworks, Chester Springs, PA WUSS2015 Paper 84 Building and Customizing a CDISC Compliance and Data Quality Application Wayne Zhong, Accretion Softworks, Chester Springs, PA ABSTRACT Creating your own SAS application to perform CDISC

More information

BUSINESS VALUE OF SEMANTIC TECHNOLOGY

BUSINESS VALUE OF SEMANTIC TECHNOLOGY BUSINESS VALUE OF SEMANTIC TECHNOLOGY Preliminary Findings Industry Advisory Council Emerging Technology (ET) SIG Information Sharing & Collaboration Committee July 15, 2005 Mills Davis Managing Director

More information

11. Extension Potential Financial Benefits

11. Extension Potential Financial Benefits 11. Extension Potential Financial Benefits Estimating the financial value of using electronic health records (EHR) for clinical research is fraught with difficulties for a number of reasons, some of which

More information

Open Source egovernment Reference Architecture Osera.modeldriven.org. Copyright 2006 Data Access Technologies, Inc. Slide 1

Open Source egovernment Reference Architecture Osera.modeldriven.org. Copyright 2006 Data Access Technologies, Inc. Slide 1 Open Source egovernment Reference Architecture Osera.modeldriven.org Slide 1 Caveat OsEra and the Semantic Core is work in progress, not a ready to use capability Slide 2 OsEra What we will cover OsEra

More information

Data Standards Panel Discussion November 30, 2011

Data Standards Panel Discussion November 30, 2011 Data Standards Panel Discussion November 30, 2011 1 Data Standards Panel Discussion Panel Members Chuck Cooper, MD, CDER, FDA Margaret Haber, National Cancer Institute, NIH Dana Pinchotti, American College

More information

Udo Siegmann member of e3c, CDISC Sen. Dir. Acc. Management PAREXEL

Udo Siegmann member of e3c, CDISC Sen. Dir. Acc. Management PAREXEL Innovative Medicines Technological Platform Udo Siegmann member of e3c, CDISC Sen. Dir. Acc. Management PAREXEL Facts about PAREXEL Full service CRO (Clinical Research Organisation) Involved in more than

More information

PharmaSUG2010 - Paper CD13

PharmaSUG2010 - Paper CD13 PharmaSUG2010 - Paper CD13 In-Depth Review of Validation Tools to Check Compliance of CDISC SDTM-Ready Clinical Datasets Bhavin Busa, Cubist Pharmaceuticals, Inc., Lexington, MA Kim Lindfield, Cubist Pharmaceuticals,

More information

DISCOVERING RESUME INFORMATION USING LINKED DATA

DISCOVERING RESUME INFORMATION USING LINKED DATA DISCOVERING RESUME INFORMATION USING LINKED DATA Ujjal Marjit 1, Kumar Sharma 2 and Utpal Biswas 3 1 C.I.R.M, University Kalyani, Kalyani (West Bengal) India sic@klyuniv.ac.in 2 Department of Computer

More information

Analysis Datasets in Vaccine Clinical Trials

Analysis Datasets in Vaccine Clinical Trials Analysis Datasets in Vaccine Clinical Trials Jingyee Kou, Ph.D. CBER/OBE PhUSE One-Day Event, Raleigh, NC. September 14, 2011 Disclaimer The findings and conclusions in this presentation have not been

More information

An Introduction to CDISC: Available CDISC Standards and Models and How SAS Supports These

An Introduction to CDISC: Available CDISC Standards and Models and How SAS Supports These An Introduction to CDISC: Available CDISC Standards and Models and How SAS Supports These Dave Handelsman Principal Strategist, Clinical R&D, SAS October 2005 Copyright 2005, SAS Institute Inc. All rights

More information

We have big data, but we need big knowledge

We have big data, but we need big knowledge We have big data, but we need big knowledge Weaving surveys into the semantic web ASC Big Data Conference September 26 th 2014 So much knowledge, so little time 1 3 takeaways What are linked data and the

More information

CDISC Journal. The Major Impacts of CDISC on Clinical Data Lifecycle. By Chengxin Li, Nancy Bauer, Boehringer Ingelheim Pharmaceuticals, Inc.

CDISC Journal. The Major Impacts of CDISC on Clinical Data Lifecycle. By Chengxin Li, Nancy Bauer, Boehringer Ingelheim Pharmaceuticals, Inc. CDISC Journal Clinical Data Interchange Standards Consortium oc tober 2012 The Major Impacts of CDISC on Clinical Data Lifecycle By Chengxin Li, Nancy Bauer, Boehringer Ingelheim Pharmaceuticals, Inc.

More information

Development of an open metadata schema for Prospective Clinical Research (openpcr)

Development of an open metadata schema for Prospective Clinical Research (openpcr) Supplementary Web Material Development of an open metadata schema for Prospective Clinical Research (openpcr) in China A. Methods We used Singapore Framework for Dublin Core Application Profiles (DCAP),

More information

Executive Summary for deliverable D7.1: Establish specification for data acquisition and standards used including a concept for local interfaces

Executive Summary for deliverable D7.1: Establish specification for data acquisition and standards used including a concept for local interfaces Electronic Health Records for Clinical Research Executive Summary for deliverable D7.1: Establish specification for data acquisition and standards used including a concept for local interfaces Project

More information

Business & Decision Life Sciences

Business & Decision Life Sciences Business & Decision Life Sciences Define-it: Demo webinar Anne-Sophie Bekx / 20th May 2014 INSERT COMPANY LOGO IN MASTER SLIDE HERE History of Define.xml Define-it Software Demo Define-it versions Q &

More information

The ADaM Solutions to Non-endpoints Analyses

The ADaM Solutions to Non-endpoints Analyses The ADaM Solutions to Non-endpoints Analyses ABSTRACT Chengxin Li, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA There always exist some analyses for non endpoints in the study. These

More information

Medical Decision Logic, Inc.

Medical Decision Logic, Inc. Medical Decision Logic, Inc. mdlogix Registries and Health Science: Applied Health Informatics Presentation Plan Mission, Goals, and Vision Theoretical Foundation (models) Pragmatic Foundation (cases)

More information

Technical Leadership Committee

Technical Leadership Committee CDISC Technical Leadership Committee Team Updates CDISC Interchange, November 2009 Baltimore Strength through collaboration. As a catalyst t for productive collaboration, CDISC brings together th individuals

More information

Alcohol Use Disorder Identification Test Self-Report Version (AUDIT-SR)

Alcohol Use Disorder Identification Test Self-Report Version (AUDIT-SR) Alcohol Use Disorder Identification Test Self-Report Version (AUDIT-SR) Questionnaire Supplement to the Study Data Tabulation Model Implementation Guide for Human Clinical Trials Prepared by TBI Standards

More information

Achille Felicetti" VAST-LAB, PIN S.c.R.L., Università degli Studi di Firenze!

Achille Felicetti VAST-LAB, PIN S.c.R.L., Università degli Studi di Firenze! 3D-COFORM Mapping Tool! Achille Felicetti" VAST-LAB, PIN S.c.R.L., Università degli Studi di Firenze!! The 3D-COFORM Project! Work Package 6! Tools for the semi-automatic processing of legacy information!

More information

Semantic Knowledge Management System. Paripati Lohith Kumar. School of Information Technology

Semantic Knowledge Management System. Paripati Lohith Kumar. School of Information Technology Semantic Knowledge Management System Paripati Lohith Kumar School of Information Technology Vellore Institute of Technology University, Vellore, India. plohithkumar@hotmail.com Abstract The scholarly activities

More information

Sustainable Development with Geospatial Information Leveraging the Data and Technology Revolution

Sustainable Development with Geospatial Information Leveraging the Data and Technology Revolution Sustainable Development with Geospatial Information Leveraging the Data and Technology Revolution Steven Hagan, Vice President, Server Technologies 1 Copyright 2011, Oracle and/or its affiliates. All rights

More information

Meeting of the Group of Experts on Business Registers. Brussels, 21 23 September 2015. Transforming the ABS Business Register

Meeting of the Group of Experts on Business Registers. Brussels, 21 23 September 2015. Transforming the ABS Business Register Meeting of the Group of Experts on Business Registers Brussels, 21 23 September 2015 Name of author(s): Luisa Ryan, Jenny Foster and John Machin Organization: Australian Bureau of Statistics Session No.

More information