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Principles of Biomedical Informatics - 2nd Edition - ISBN: 9780124160194, 9780123914620

Principles of Biomedical Informatics

2nd Edition

Author: Ira Kalet, PhD
Hardcover ISBN: 9780124160194
eBook ISBN: 9780123914620
Imprint: Academic Press
Published Date: 30th September 2013
Page Count: 708
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This second edition of a pioneering technical work in biomedical informatics provides a very readable treatment of the deep computational ideas at the foundation of the field. Principles of Biomedical Informatics, 2nd Edition is radically reorganized to make it especially useable as a textbook for courses that move beyond the standard introductory material. It includes exercises at the end of each chapter, ideas for student projects, and a number of new topics, such as:
• tree structured data, interval trees, and time-oriented medical data and their use
• On Line Application Processing (OLAP), an old database idea that is only recently coming of age and finding surprising importance in biomedical informatics
• a discussion of nursing knowledge and an example of encoding nursing advice in a rule-based system
• X-ray physics and algorithms for cross-sectional medical image reconstruction, recognizing that this area was one of the most central to the origin of biomedical computing
• an introduction to Markov processes, and
• an outline of the elements of a hospital IT security program, focusing on fundamental ideas rather than specifics of system vulnerabilities or specific technologies.

It is simultaneously a unified description of the core research concept areas of biomedical data and knowledge representation, biomedical information access, biomedical decision-making, and information and technology use in biomedical contexts, and a pre-eminent teaching reference for the growing number of healthcare and computing professionals embracing computation in health-related fields.

As in the first edition, it includes many worked example programs in Common LISP, the most powerful and accessible modern language for advanced biomedical concept representation and manipulation.

The text also includes humor, history, and anecdotal material to balance the mathematically and computationally intensive development in many of the topic areas. The emphasis, as in the first edition, is on ideas and methods that are likely to be of lasting value, not just the popular topics of the day.

Ira Kalet is Professor Emeritus of Radiation Oncology, and of Biomedical Informatics and Medical Education, at the University of Washington. Until retiring in 2011 he was also an Adjunct Professor in Computer Science and Engineering, and Biological Structure. From 2005 to 2010 he served as IT Security Director for the University of Washington School of Medicine and its major teaching hospitals. He has been a member of the American Medical Informatics Association since 1990, and an elected Fellow of the American College of Medical Informatics since 2011. His research interests include simulation systems for design of radiation treatment for cancer, software development methodology, and artificial intelligence applications to medicine, particularly expert systems, ontologies and modeling.

Key Features

  • Develops principles and methods for representing biomedical data, using information in context and in decision making, and accessing information to assist the medical community in using data to its full potential
  • Provides a series of principles for expressing biomedical data and ideas in a computable form to integrate biological, clinical, and public health applications
  • Includes a discussion of user interfaces, interactive graphics, and knowledge resources and reference material on programming languages to provide medical informatics programmers with the technical tools to develop systems


Advanced students and faculty in computing, bioinformatics and medical informatics academic programs; software engineers and programmers working in biotechnology, pharmaceutical, and medical records companies, and the medical imaging industry.

Table of Contents

  • Dedication
  • Preface to the Second Edition
  • Foreword From the First Edition
  • Preface from the First Editon
  • List of figures
  • List of Tables
  • 1: Biomedical Data
    • 1.1 The Nature and Representation of Biomedical Data
    • 1.2 Objects, Metadata, and Serialization
    • 1.3 Database Concepts and Systems
    • 1.4 Data Quality
    • 1.5 Data, Information, and Knowledge
    • 1.6 Summary
    • 1.7 Exercises
  • 2: Symbolic Biomedical Knowledge
    • 2.1 Biomedical Theories and Computer Programs
    • 2.2 Logic and Inference Systems
    • 2.3 Frames, Semantic Nets, and Ontologies
    • 2.4 Description Logics
    • 2.5 Summary
    • 2.6 Exercises
  • 3: Probabilistic Biomedical Knowledge
    • 3.1 Probability and Statistics
    • 3.2 Bayes’ Rule, Bayes Nets, and Probabilistic Inference
    • 3.3 Utility and Decision Modeling
    • 3.4 Information Theory
    • 3.5 Summary
    • 3.6 Exercises
  • 4: Biomedical Information Access
    • 4.1 Information Retrieval Systems
    • 4.2 Beyond Text Documents
    • 4.3 Networks and Biomedical Data Communication
    • 4.4 Summary
    • 4.5 Exercises
  • 5: Computational Models and Methods
    • 5.1 Computing with Genes, Proteins, and Cells
    • 5.2 Search
    • 5.3 Natural Language Processing
    • 5.4 State Machines and Dynamic Models
    • 5.5 Stochastic Processes
    • 5.6 Summary
    • 5.7 Exercises
  • 6: Biomedical Data, Knowledge, and Systems in Context
    • 6.1 A Bit of Personal History and Perspective
    • 6.2 Medical Device Safety
    • 6.3 System and Data Security
    • 6.4 Summary
    • 6.5 Exercises
  • 7: Epilogue
    • 7.1 The Halting Problem—A Metaphoric Version
    • 7.2 Where Do New Ideas Come From?
    • 7.3 Making A Difference
  • Appendix A: Notes on Lisp, Other Languages, and Resources
    • A.1 Lisp Notes
    • A.2 Other Programming Languages
    • A.3 Other Resources
    • A.4 Exercises
  • Bibliography
  • Index


No. of pages:
© Academic Press 2013
30th September 2013
Academic Press
Hardcover ISBN:
eBook ISBN:

About the Author

Ira Kalet, PhD

Ira Kalet, PhD

Affiliations and Expertise

Department of Radiation Oncology, University of Washington Medical Center, Seattle, USA


"Kalet…explain(s) the principles of biomedical informatics by showing how to write computer programs that implement them. He covers biomedical data; symbolic biomedical knowledge; probabilistic biomedical knowledge; biomedical information access; computational models and methods; and biomedical data, knowledge, and systems in context. He has updated the 2009 first edition, maintaining his focus on fundamentals." --Reference & Research Book News, December 2013

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