Health Informatics. Founding Series Editors Kathryn J. Hannah Marion J. Ball

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2 Health Informatics Founding Series Editors Kathryn J. Hannah Marion J. Ball

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4 Rachel L. Richesson James E. Andrews Editors Clinical Research Informatics

5 Editors Rachel L. Richesson, Ph.D., MPH Division of Informatics Duke University School of Nursing Durham NC USA James E. Andrews, Ph.D. Director and Associate Professor College of Arts and Sciences School of Information University of South Florida Tampa FL USA ISBN e-isbn DOI / Springer London Dordrecht Heidelberg New York British Library Cataloguing in Publication Data A catalogue record for this book is available from the British Library Library of Congress Control Number: Springer-Verlag London Limited 2012 Apart from any fair dealing for the purposes of research or private study, or criticism or review, as permitted under the Copyright, Designs and Patents Act 1988, this publication may only be reproduced, stored or transmitted, in any form or by any means, with the prior permission in writing of the publishers, or in the case of reprographic reproduction in accordance with the terms of licences issued by the Copyright Licensing Agency. Enquiries concerning reproduction outside those terms should be sent to the publishers. The use of registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant laws and regulations and therefore free for general use. Product liability: The publisher can give no guarantee for information about drug dosage and application thereof contained in this book. In every individual case the respective user must check its accuracy by consulting other pharmaceutical literature. Printed on acid-free paper Springer is part of Springer Science+Business Media (

6 Contents Part I Contexts of Clinical Research Informatics 1 Introduction to Clinical Research Informatics Rachel L. Richesson and James E. Andrews 2 From Notations to Data: The Digital Transformation of Clinical Research Christopher G. Chute 3 The Clinical Research Environment Philip R.O. Payne 4 Methodological Foundations of Clinical Research Antonella Bacchieri and Giovanni Della Cioppa 5 Informatics Approaches to Participant Recruitment Chunhua Weng and Peter J. Embi 6 The Evolving Role of Consumers J. David Johnson and James E. Andrews 7 Clinical Research in the Postgenomic Era Stephane M. Meystre, Scott P. Narus, and Joyce A. Mitchell Part II Data Management and Systems in Clinical Research 8 Clinical Research Information Systems Prakash M. Nadkarni, Luis N. Marenco, and Cynthia A. Brandt 9 Study Protocol Representation Ida Sim and Joyce C. Niland 10 Data Quality in Clinical Research Meredith Nahm 11 Patient-Reported Outcome Data Robert O. Morgan and Kavita R. Sail v

7 vi Contents 12 Biobanking Challenges and Informatics Opportunities Elizabeth J. Horn and Sharon F. Terry 13 Patient Registries Rachel L. Richesson and Kendra Vehik Part III Knowledge Representation and Discovery 14 Knowledge Representation and Ontologies Kin Wah Fung and Olivier Bodenreider 15 Nonhypothesis-Driven Research: Data Mining and Knowledge Discovery Mollie R. Cummins 16 Natural Language Processing, Electronic Health Records, and Clinical Research Feifan Liu, Chunhua Weng, and Hong Yu Part IV The Future of Clinical Research, Health, and Clinical Research Informatics 17 Data Sharing: Electronic Health Records and Research Interoperability Rebecca Daniels Kush 18 Standards Development and the Future of Research Data Sources, Interoperability, and Exchange W. Ed Hammond and Rachel L. Richesson 19 Pharmacovigilance A.C. (Kees) van Grootheest and Rachel L. Richesson 20 Clinical Trials Registries and Results Databases Karmela Krleža-Jerić 21 Future Directions in Clinical Research Informatics Peter J. Embi Index

8 Contributors James E. Andrews, Ph.D. School of Information, College of Arts and Sciences, University of South Florida, Tampa, FL, USA Antonella Bacchieri, M.S. Department of Biostatistics and Data Management, Research and Development, Sigma-tau Industrie Farmaceutiche Riunite S.p.A., Pomezia, Rome, Italy Olivier Bodenreider, M.D., Ph.D. Lister Hill National Center for Biomedical Communications, US National Library of Medicine, National Institutes of Health, Bethesda, MD, USA Cynthia A. Brandt, M.D., MPH Yale Center for Medical Informatics, Emergency Medicine, Yale University, New Haven, CT, USA Department of Anesthesiology, VA Connecticut Healthcare System, New Haven, CT, USA Christopher G. Chute, M.D., DrPH Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA Mollie R. Cummins, Ph.D., APRN College of Nursing, University of Utah, Salt Lake City, UT, USA Giovanni Della Cioppa, M.D. Global Clinical Research and Development, Vaccines, Novartis Vaccines and Diagnostics, Siena, Italy Peter J. Embi, M.D., M.S. Department of Biomedical Informatics and Internal Medicine, The Ohio State University Medical Center, Columbus, OH, USA Kin Wah Fung, M.D., M.S., M.A. Lister Hill National Center for Biomedical Communications, US National Library of Medicine, National Institutes of Health, Bethesda, MD, USA vii

9 viii Contributors W. Ed Hammond, Ph.D. Duke Center for Health Informatics, Duke Translation Medicine Institute, Durham, NC, USA Applied Informatics Research, Duke Health Technology Solutions Biomedical Informatics Core, Duke Translational Medicine Institute Department of Community and Family Medicine, School of Medicine Department of Biomedical Engineering, Pratt School of Engineering Fuqua School of Business, Duke University, Durham, NC, USA Elizabeth J. Horn, Ph.D., MBI Genetic Alliance Registry & BioBank, Genetic Alliance, Washington, DC, USA J. David Johnson, Ph.D., M.A., B.S. Department of Communication, University of Kentucky, Lexington, KY, USA Karmela Krleža-Jeri, M.D., M.Sc., D.Sc. Knowledge Translation, Canadian Institutes of Health Research, Ottawa, ON, Canada Department of Epidemiology and Community Health, Medical Faculty, University of Ottawa, Ottawa, ON, Canada Rebecca Daniels Kush, Ph.D., B.S. Executive Operations, CDISC, Austin, TX, USA Feifan Liu, Ph.D. Department of Electric Engineering and Computer Science, University of Wisconsin Milwaukee, Milwaukee, WI, USA Luis N. Marenco, M.D. Yale Center for Medical Informatics, Yale University, New Haven, CT, USA Stephane M. Meystre, M.D., Ph.D. Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA Joyce A. Mitchell, Ph.D. Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA Robert O. Morgan, Ph.D. Department of Management, Policy and Community Health, University of Texas School of Public Health, Houston, TX, USA Prakash M. Nadkarni, M.D. Center for Medical Informatics, Yale University School of Medicine, New Haven, CT, USA Meredith Nahm, Ph.D. Informatics, Duke Translational Medicine Institute, Duke University, Durham, NC, USA Scott P. Narus, Ph.D. Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA Joyce C. Niland, Ph.D. Division of Information Sciences, Beckman Research Institute, City of Hope, Duarte, CA, USA

10 Contributors ix Philip R.O. Payne, Ph.D. Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA Rachel L. Richesson, Ph.D., MPH Department of Informatics, Duke University, School of Nursing, Durham, NC, USA Kavita R. Sail, Ph.D. Department of Health Care Informatics, McKesson/US Oncology Specialty Care Unit, The Woodlands, TX, USA Ida Sim, M.D., Ph.D. Department of Medicine, University of California San Francisco, San Francisco, CA, USA Sharon F. Terry, M.A. Genetic Alliance, Registry and Biobank, Genetic Alliance, Washington, DC, USA A.C. (Kees) van Grootheest, M.D., Ph.D. Mathematics and Natural Sciences, Netherlands Pharmacovigilance Centre, s-hertogenbosch, the Netherlands Department of Pharmacy, University of Groningen, s-hertogenbosch, the Netherlands Kendra Vehik, Ph.D., MPH Department of Pediatrics, Pediatrics Epidemiology Center, University of South Florida, Tampa, FL, USA Chunhua Weng, Ph.D. Department of Biomedical Informatics, Columbia University, New York, NY, USA Hong Yu, Ph.D. Department of Electric Engineering and Computer Science, University of Wisconsin Milwaukee, Milwaukee, WI, USA

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12 Part I Contexts of Clinical Research Informatics

13 Chapter 1 Introduction to Clinical Research Informatics Rachel L. Richesson and James E. Andrews Abstract This chapter provides essential definitions and overviews important constructs and methods within the emerging subdomain of clinical research informatics. The chapter also highlights theoretical and practical contributions from other disciplines. This chapter sets the tone and scope for the text, highlights important themes, and describes the content and organization of chapters. Keywords Clinical research informatics definition CRI Theorem of informatics American Medical Informatics Association Biomedical informatics Overview The documentation, representation, and exchange of information in clinical research are inherent to the very notion of research as a controlled and reproducible set of methods for scientific inquiry. Clinical research is the branch of medical science that investigates the safety and effectiveness of medications, devices, diagnostic products, and treatment regimens intended for human use in the prevention, diagnosis, treatment, or management of a disease. Clinical research enables new understanding and practices for prevention, diagnosis, or treatment of a disease or its symptoms. Contemporary clinical research actually represents relatively recent application of statistics to medicine and the acceptance of randomized controlled clinical trials as the gold standard [ 1 ] in this last half-century. Clinical research has been characterized as a discipline resting on three pillars of principle and practice R.L. Richesson, Ph.D., MPH (*) Division of Informatics, Duke University School of Nursing, 311 Trent Drive, Durham, NC 27710, USA rachel.richesson@dm.duke.edu J.E. Andrews, Ph.D. School of Information, College of Arts and Sciences, University of South Florida, 4202 E. Fowler Ave, CIS 1040, Tampa, FL , USA jimandrews@usf.edu R.L. Richesson, J.E. Andrews (eds.), Clinical Research Informatics, Health Informatics, DOI / _1, Springer-Verlag London Limited

14 4 R.L. Richesson and J.E. Andrews related to control, mensuration, and analysis [ 2 ], though these can be more modernly interpreted as a triad of expertise in medicine, statistics, and logistics [ 3 ]. Clinical research informatics (CRI), then, is the application of informatics principles and techniques to support the spectrum of activities and business processes that instantiate clinical research. Informatics, as somewhat crudely defined as the intersection of information and computer science with a health-related discipline, has a foundation that has drawn from many well-established, theory-based disciplines, including computer science, library and information science, cognitive science, psychology, and sociology. The newly articulated yet fundamental theorem of informatics [4 ] states that humans plus information technology should function and perform better together than humans alone, and so informatics is a source for supportive technologies and tools that enhance but not replace unreservedly human processes. The US National Institutes of Health offer a comprehensive and widely accepted definition for clinical research that includes a spectrum of populations, objectives, methods, and activities. Specifically, this broad definition states that clinical research is patient-oriented research conducted with human subjects (or on material of human origin that can be linked to an individual) [ 5 ]. Under this definition, clinical research includes investigation of the mechanisms of human disease, therapeutic interventions, clinical trials, development of new technologies, epidemiology, behavioral studies, and outcomes and health services research. This definition was used by all authors in this text to scope the content, so readers will see a broad overview of important informatics topics and constructs, as they apply to this wide spectrum of research objectives, participants, stakeholders, and activities. Given this broad definition, clearly the challenges in clinical research and the opportunities for informatics support arise from many different objectives and requirements, including the need for optimal protocol design, regulatory compliance, sufficient patient recruitment, efficient protocol management, and data collection and acquisition; data storage, transfer, processing, and analysis; and impeccable patient safety throughout. Regardless of clinical domain or study design, highquality data collection and standard formalized data representation are critical to the fundamental notion of reproducibility of results. In addition to explicit and suitable data collection methods for reliability, strong study design and conduct (sampling in particular) are necessary for the generalizability of research findings. In the age of an electronic data deluge, standards also take on critical importance and can facilitate data sharing, knowledge generation, and new discovery using existing data sets and resources. Contexts and Attempts to Define Clinical Research Informatics The driving forces for the rapid emergence of the CRI domain include advances in information technology and a mass of grassroots innovations that are enabling new data collection methods and integration of multiple data sources to generate new

15 1 Introduction to Clinical Research Informatics 5 hypotheses, more efficient research, and patient safety in all phases of research and public health. While the range of computer applications employed in clinical research settings might be (superficially) seen as a set of service or support activities, the practice of CRI extends beyond mere information technology support for clinical research. The needs and applications of information management and data and communication technologies to support research run across medical domains, care and research settings, and research designs. Because these issues and tools are shared across various settings and domains, fundamental research to develop theory-based and generalizable applications and systems is in order. Original research will afford an evidence base for information and communications technologies that meaningfully address the business needs of research and also streamline, change, and improve the business of research itself. As a relatively new field, but driven by maturing professional and research communities, CRI is just at the point where a defined research agenda is beginning to coalesce. As this research agenda is articulated, standards and best practices for research will emerge, as will standards for education and training in the field. Embi and Payne (2009) present a definition for CRI as the sub-domain of biomedical informatics concerned with the development, application, and evaluation of theories, methods, and systems to optimize the design and conduct of clinical research and the analysis, interpretation, and dissemination of the information generated [6 ]. An illustrative but nonexhaustive list of CRI focus areas and activities augment this American Medical Informatics Association (AMIA)-developed definition: evaluation and modeling of clinical and translational research workflow; social and behavioral studies involving clinical research; designing optimal humancomputer interaction models for clinical research applications; improving and evaluating information capture and data; flow in clinical research; optimizing research site selection, investigator, and subject recruitment; knowledge engineering and standards development as applied to clinical research; facilitating and improving research reporting to regulatory agencies; and enhancing clinical and research data mining, integration, and analysis. The definition and illustrative activities emerged from in-person and virtual meetings and interviews with self-identified CRI practitioners within the AMIA organization. The scope and number of activities, and the information problems and priorities to be addressed, will obviously evolve over time as in any field. Moreover, a single professional or educational home for CRI, and as such a source to develop a single consensus and more precise definition, is lacking at present and likely unachievable given the multidisciplinary and multinational and multicultural scope of CRI activities. What is important to note is that this is all reflective of the bottom-up development of this area, reflecting the applications of information technology that have been needed and that are in use. The first references to what is now known as clinical research informatics go back to the 1960s and highlight the inevitable use of computers to support data collection and analysis in research [ 7 ]. The use of clinical databases for research inquiry was first established in the late 1960s, and by the next decade more than 40 years ago there were at least a handful of clinical information systems being used for research. This history is well described in Collen in a 1990 historical review. In short