Kalet / PhD Principles of Biomedical Informatics

1. Auflage 2008
ISBN: 978-0-08-055794-6
Verlag: Elsevier Science & Techn.
Format: EPUB
Kopierschutz: 6 - ePub Watermark

E-Book, Englisch, 504 Seiten

This book provides a foundation for understanding the fundamentals of biomedical informatics, which deals with the storage, retrieval, and use of biomedical data for biological problem solving and medical decision making. It covers the application of these principles to the three main biomedical domains of basic biology, clinical medicine, and public health. The author offers a coherent summary, focusing on the three core concept areas of biomedical data and knowledge representation: biomedical information access, biomedical decision making, and information and technology use in biomedical contexts.
* 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

Autoren/Hrsg.

Kalet, Ira J.

PhD,

Inhaltsverzeichnis

1;Front Cover;1
2;Principles of Biomedical Informatics;4
3;Copyright;5
4;Dedication;6
5;Table of Contents;8
6;Foreword;14
7;Preface;18
8;Part I: Foundations of Biomedical Informatics;28
8.1;Chapter 1. Biomedical Data;30
8.1.1;1.1 The Nature and Representation of Biomedical Data;33
8.1.1.1;1.1.1 What Can Be Represented in a Computer?;40
8.1.1.2;1.1.2 DNA and the Genetic Code;54
8.1.1.3;1.1.3 Anatomy;64
8.1.1.4;1.1.4 Medical Laboratory Data;65
8.1.1.5;1.1.5 Medical Images;69
8.1.1.6;1.1.6 Metadata;77
8.1.2;1.2 Objects, Metadata, and Serialization;80
8.1.2.1;1.2.1 A Simple Solution Using Tags (Keywords);81
8.1.2.2;1.2.2 An Object-oriented Design;82
8.1.2.3;1.2.3 A Better Solution Using Meta-objects;92
8.1.2.4;1.2.4 Medical Images: Incorporating Binary Data;99
8.1.3;1.3 XML;104
8.1.4;1.4 Database Systems and Ideas;111
8.1.4.1;1.4.1 The Relational Model;112
8.1.4.2;1.4.2 The Entity–Attribute–Value Model;119
8.1.5;1.5 Data Quality;120
8.1.6;1.6 Data, Information and Knowledge;122
8.1.7;1.7 Summary;124
8.2;Chapter 2. Symbolic Biomedical Knowledge;126
8.2.1;2.1 Biomedical Theories and Computer Programs;128
8.2.1.1;2.1.1 A World Class Reasoning Example;128
8.2.1.2;2.1.2 Biological Examples;129
8.2.1.3;2.1.3 Symbolic Theories;129
8.2.2;2.2 Logic and Inference Systems;132
8.2.2.1;2.2.1 Predicate Calculus;133
8.2.2.2;2.2.2 Unsound Inference: Abduction and Induction;151
8.2.2.3;2.2.3 First Order Logic;152
8.2.2.4;2.2.4 Rule-based Programming for FOL;160
8.2.2.5;2.2.5 Limitations of FOL;166
8.2.3;2.3 Frames, Semantic Nets, and Ontologies;169
8.2.3.1;2.3.1 A Simple Frame System;170
8.2.3.2;2.3.2 Extensions to Frame Systems;186
8.2.3.3;2.3.3 Frame System Implementations, Interfaces, and APIs;189
8.2.3.4;2.3.4 Frames and Object-oriented Programming Languages;189
8.2.4;2.4 Description Logics;190
8.2.4.1;2.4.1 Description Logic Languages;193
8.2.4.2;2.4.2 Examples from GALEN;194
8.2.4.3;2.4.3 The Semantic Web;197
8.2.4.4;2.4.4 Back to the Future;200
8.2.5;2.5 Search;200
8.2.5.1;2.5.1 A General Framework for Search;201
8.2.5.2;2.5.2 Uninformed Search Strategies;205
8.2.5.3;2.5.3 Informed Search Strategies;207
8.2.5.4;2.5.4 Path Search;209
8.2.6;2.6 Summary;210
8.3;Chapter 3. Probabilistic Biomedical Knowledge;212
8.3.1;3.1 Probability and Statistics;213
8.3.1.1;3.1.1 Probability;213
8.3.1.2;3.1.2 Statistics;214
8.3.1.3;3.1.3 The Laws of Probability;215
8.3.1.4;3.1.4 Conditional Probability;217
8.3.1.5;3.1.5 Independence;218
8.3.1.6;3.1.6 Random Variables and Estimation;219
8.3.2;3.2 Application and Generalization of Bayes’ rule;226
8.3.2.1;3.2.1 Simple Bayesian Inference;228
8.3.2.2;3.2.2 Non-Boolean Variables;229
8.3.2.3;3.2.3 Bayes Nets;230
8.3.3;3.3 Utility and Decision Modeling;234
8.3.3.1;3.3.1 A Decision Analysis Vignette;235
8.3.3.2;3.3.2 Graph Structure and Probability Assignment;236
8.3.3.3;3.3.3 Determining Utilities;237
8.3.3.4;3.3.4 Computation of Expected Values;238
8.3.4;3.4 Information Theory;240
8.3.4.1;3.4.1 Encoding of Messages;240
8.3.4.2;3.4.2 Entropy and Information;243
8.3.4.3;3.4.3 Efficient Encoding;244
8.3.4.4;3.4.4 Error Detection and Correction;247
8.3.4.5;3.4.5 Information Theory in Biology and Medicine;247
8.3.5;3.5 Summary;248
8.4;Chapter 4. Biomedical Information Access;250
8.4.1;4.1. Information Retrieval Systems;250
8.4.2;4.2. IR System Design;254
8.4.2.1;4.2.1 Indexing;254
8.4.2.2;4.2.2 Processing Queries;259
8.4.2.3;4.2.3 Searching and Matching;260
8.4.2.4;4.2.4 Ranking the Results;260
8.4.2.5;4.2.5 Performance Evaluation;261
8.4.3;4.3 Intelligent Query Processing;262
8.4.4;4.4 Network Access to Document Repositories;262
8.4.5;4.5 Natural Language Processing;273
8.4.6;4.6 Beyond Text Documents;275
8.4.6.1;4.6.1 Biomedical Images;276
8.4.6.2;4.6.2 Electronic Medical Records;277
8.4.7;4.7 Summary;277
9;Part II: Biomedical Ideas and Computational Realizations;278
9.1;Chapter 5. Computing With Genes, Proteins, and Cells;280
9.1.1;5.1 Getting Data From Files;282
9.1.2;5.2 Computing With DNA Sequences;286
9.1.3;5.3 Mapping Genes to Proteins;291
9.1.4;5.4 Computing With Protein Sequences;295
9.1.4.1;5.4.1 Representing Amino Acid and Proteins;295
9.1.4.2;5.4.2 Simple Properties of Proteins From Sequence Data;298
9.1.4.3;5.4.3 Amino Acid Profiles;299
9.1.5;5.5 The Gene Ontology;304
9.1.6;5.6 Biochemical Pathways;307
9.1.6.1;5.6.1 Searching for Pathways;308
9.1.6.2;5.6.2 Biochemical Reachability Logic;314
9.1.7;5.7 Simulation With State Machines;318
9.1.7.1;5.7.1 State Machines;318
9.1.7.2;5.7.2 A Simple State Machine;320
9.1.7.3;5.7.3 Simulating the Cell Cycle in Yeast;324
9.1.8;5.8 Summary;329
9.2;Chapter 6. Modeling Biological Structure;330
9.2.1;6.1 The UW Foundational Model of Anatomy;331
9.2.1.1;6.1.1 The Components of the FMA;331
9.2.1.2;6.1.2 Representing Anatomical Relations in the FMA;332
9.2.1.3;6.1.3 Metaclasses;332
9.2.1.4;6.1.4 The part-of Relationship;335
9.2.2;6.2 A Simple Network Interface – the FMS;335
9.2.3;6.3 Semantic Consistency Checking and the FMA;342
9.2.3.1;6.3.1 The Lymphatic System: An Example;344
9.2.3.2;6.3.2 Current State of the Lymphatics in the FMA;346
9.2.4;6.4 Summary;350
9.3;Chapter 7. Drug Interactions;352
9.3.1;7.1 Drug Information Catalogs;354
9.3.2;7.2 Reasoning About Pharmacokinetics;358
9.3.2.1;7.2.1 Procedural Knowledge About Enzymatic Metabolism;360
9.3.2.2;7.2.2 A Rule-based Drug Interaction System;361
9.3.2.3;7.2.3 Truth Maintenance Systems;364
9.3.2.4;7.2.4 A Drug Interactions Theory with Justifications;367
9.3.2.5;7.2.5 Evidence-based Reasoning;369
9.3.3;7.3 Reasoning About Pharmacodynamics;372
9.3.4;7.4 Summary;374
9.4;Chapter 8. Medical Data Communication;376
9.4.1;8.1 EMR Systems and PACS;377
9.4.1.1;8.1.1 EMR Systems;377
9.4.1.2;8.1.2 Medical Images and PACS;379
9.4.2;8.2 Networks and Protocols;379
9.4.2.1;8.2.1 Network Architecture;379
9.4.2.2;8.2.2 Network Client and Server Design;381
9.4.3;8.3 HL7;383
9.4.3.1;8.3.1 The HL7 Message Exchange Protocol;383
9.4.3.2;8.3.2 HL7 Message Structure;384
9.4.3.3;8.3.3 Scanning HL7 Messages;386
9.4.3.4;8.3.4 HL7 Message Field Content;388
9.4.4;8.4 DICOM: Medical Image Information Agents;391
9.4.4.1;8.4.1 A Short History of DICOM;391
9.4.4.2;8.4.2 About the DICOM Standard;393
9.4.5;8.5 How to Implement DICOM;397
9.4.5.1;8.5.1 The DICOM State Machine;398
9.4.5.2;8.5.2 Parsing and Generation of PDUs;407
9.4.5.3;8.5.3 Parsing and Generation of Commands and Data;413
9.4.5.4;8.5.4 How It All Turned Out;417
9.4.6;8.6 Summary;418
9.5;Chapter 9. Cancer Radiotherapy Planning;420
9.5.1;9.1. Radiation Therapy;421
9.5.2;9.2. Radiotherapy Planning Software;422
9.5.3;9.3. Locating the Target;425
9.5.3.1;9.3.1 Computing the CTV;427
9.5.3.2;9.3.2 Computing the PTV;433
9.5.4;9.4. Influence Diagrams in RTP;440
9.5.5;9.5 Summary;441
9.6;Chapter 10. Safety and Security;444
9.6.1;10.1 A Bit of Personal History and Perspective;445
9.6.2;10.2 Some Real-Life Stories;446
9.6.2.1;10.2.1 Radiation Therapy Planning Systems;447
9.6.2.2;10.2.2 Who is Master, the Human or the Computer?;449
9.6.2.3;10.2.3 The Therac-25: A Real-Time Disaster;449
9.6.2.4;10.2.4 Prism;450
9.6.2.5;10.2.5 The UW Neutron Therapy Facility;450
9.6.2.6;10.2.6 DICOM and Internet Security;451
9.6.2.7;10.2.7 Intravenous Infusion Pumps on the Internet;451
9.6.3;10.3 Safety By Design: Radiotherapy Machines;452
9.6.3.1;10.3.1 A Simple Linac Control System;453
9.6.3.2;10.3.2 Adding a Dosimetry System;455
9.6.3.3;10.3.3 Formal and Automated Analysis;456
9.6.4;10.4 It Security in Health Care Organizations;456
9.6.5;10.5 Epilogue;458
9.7;Appendix A. Lisp Notes, Software, and Other Resources;460
9.7.1;A.1 Lisp Notes;460
9.7.1.1;A.1.1 General Notes on Lisp;460
9.7.1.2;A.1.2 CLOS and MOP;461
9.7.1.3;A.1.3 Optimization;463
9.7.1.4;A.1.4 Books on Lisp;464
9.7.2;A.2 Software;465
9.7.2.1;A.2.1 Data and Knowledge Resources;465
9.7.2.2;A.2.2 Common Lisp Systems, Libraries, and Resources;466
9.7.2.3;A.2.3 Languages and Tools for Knowledge Representation;466
9.7.2.4;A.2.4 Code from the Book;467
9.7.3;A.3 Other Resources;468
9.8;Bibliography;470
9.9;Index;486