Medical Informatics
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MEDICAL INFORMATICS Knowledge Management and Data Mining in Biomedicine INTEGRATED SERIES IN INFORMATION SYSTEMS Series Editors Professor Ramesh Sharda Prof. Dr. Stefan Vo13 Oklahoma State University Universitat Hamburg Other published titles in the series: E-BUSINESS MANAGEMENT: Integration of Web Technologies with Business Models1 Michael J. Shaw VIRTUAL CORPORATE UNIVERSITIES: A Matrix of Knowledge and Learning for the New Digital DawdWalter R.J. Baets & Gert Van der Linden SCALABLE ENTERPRISE SYSTEMS: An Introduction to Recent Advances1 edited by Vittal Prabhu, Soundar Kumara, Manjunath Kamath LEGAL PROGRAMMING: Legal Compliance for RFID and Software Agent Ecosystems in Retail Processes and Beyond1 Brian Subirana and Malcolm Bain LOGICAL DATA MODELING: What It Is and How To Do It1 Alan Chmura and J. Mark Heumann DESIGNING AND EVALUATING E-MANAGEMENT DECISION TOOLS: The Integration of Decision and Negotiation Models into Internet-Multimedia Technologies1 Giampiero E.G. Beroggi INFORMATION AND MANAGEMENT SYSTEMS FOR PRODUCT CUSTOMIZATIONI Blecker, Friedrich, Kaluza, Abdelkafi & Kreutler MEDICAL INFORMATICS Knowledge Management and Data Mining in Biomedicine edited by Hsinchun Chen Sherrilynne S. Fuller Carol Friedman William Hersh - Springer Hsinchun Chen Sherrilynne S. Fuller The University of Arizona, USA University of Washington, USA Carol Friedman William Hersh Columbia University, USA Oregon Health & Science Univ., USA Library of Congress Cataloging-in-Publication Data A C.I.P. Catalogue record for this book is available from the Library of Congress. ISBN-10: 0-387-2438 1-X (HB) ISBN- 10: 0-387-25739-X (e-book) ISBN- 13: 978-0387-24381-8 (HB) ISBN- 13: 978-0387-25739-6 (e-book) O 2005 by Springer Science+Business Media, Inc. All rights reserved. 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Printed in the United States of America. 98765432 1 SPIN 1 1055556 TABLE OF CONTENTS Editors' Biographies ..........................................................................xix Authors' Biographies .......................................................................xxiii Preface ............................................................................................xxxix UNIT I: Foundational Topics in Medical Informatics Chapter 1: Knowledge Management. Data Mining. and Text Mining in Medical Informatics .......................................................... 3 Introduction ........................................................................................................5 Knowledge Management, Data Mining, and Text Mining: An Overview ........................................................................................................6 2.1 Machine Learning and Data Analysis Paradigms ......................................7 2.2 Evaluation Methodologies ....................................................................... 11 Knowledge Management, Data Mining, and Text Mining Applications in Biomedicine ............................................................................ 12 3.1 Ontologies ............................................................................................... 13 3.2 Knowledge Management ......................................................................... 14 3.3 Data Mining and Text Mining ................................................................. 18 3.4 Ethical and Legal Issues for Data Mining ...............................................22 Summary ..........................................................................................................22 References .................................................................................................................23 Suggested Readings ..................................................................................................31 Online Resources ................................. .... ..............................................................31 Questions for Discussion ........................................................................................ 33 Chapter 2: Mapping Medical Informatics Research .............................35 1. Introduction ...................................................................................................... 37 2 . Knowledge Mapping: Literature Review ........................................................37 3 . Research Design .............................................................................................. 39 3.1 Basic Analysis ......................................................................................... 39 3.2 Content Map Analysis ............................................................................. 40 3.3 Citation Analysis ..................................................................................... 41 4 . Data Description .............................................................................................. 42 5 . Results .............................................................................................................. 44 5.1 Basic Analysis ......................................................................................... 44 5.2 Content Map Analysis ............................................................................. 47 5.3 Citation Network Analysis ...................................................................... 55 6 . Conclusion and Discussion .............................................................................. 57 7 . Acknowledgement ........................................................................................... 58 References .................................................................................................................58 Suggested Readings ..................................................................................................60 Online Resources ......................................................................................................61 Questionsfor Discussion ........................................................................................61 Chapter 3: Bioinformatics Challenges and Opportunities .................... 63 1. Introduction ...................................................................................................... 65 2 . Overview of the Field ...................................................................................... 69 2.1 Definition of Bioinformatics ................................................................... 69 2.2 Opportunities and Challenges - Informatics Perspective ........................ 70 2.3 Opportunities and Challenges - Biological Perspective .......................... 79 3 . Case Study ....................................................................................................83 3.1 Informatics Perspective - The BIOINFOMED Study and Genomic Medicine ........................................................................... 83 3.2 Biological Perspective - The BioResearch Liaison Program at the University of Washington ............................................... 85 4 . Conclusions and Discussion ............................................................................. 89 5 . Acknowledgements .......................................................................................... 91 References .................................................................................................................91 Suggested Readings ..................................................................................................92 Online Resources ...................................................................................................... 93 Questions for Discussion ..........................................................................................93 Chapter 4: Managing Information Security and Privacy in Health Care Data Mining: State of the Art ................................................................. 95 1. Introduction ......................................................................................................97 2 . Overview of Health Information Privacy and Security .................................... 98 2.1 Privacy and Healthcare Information ........................................................ 99 2.2 Security and Healthcare Information ....................................................... 99 3 . Review of the Literature: Data Mining and Privacy and Security ................................................................................................... 109 vii 3.1 General Approaches to Assuring Appropriate Use ...............................110 3.2 Specific Approaches to Achieving Data Anonymity ............................. 112 3.3 Other Issues in Emerging "Privacy Technology" ............................116 3.4 "Value Sensitive Design": A Synthetic Approach to Technological Development .............................................117