Principles of biomedical informatics

cover.jpg......Page 1
Dedication Page......Page 2
Foreword......Page 3
Preface......Page 6
Structure of the Book......Page 7
Software Design and Engineering......Page 8
Programming Languages......Page 9
How To Use This Book......Page 11
Acknowledgments......Page 12
I Foundations of Biomedical Informatics......Page 15
1 Biomedical Data......Page 17
The Nature and Representation of Biomedical Data......Page 20
What Can Be Represented in a Computer?......Page 27
DNA and the Genetic Code......Page 41
Anatomy......Page 51
Medical Laboratory Data......Page 52
Medical Images......Page 56
Metadata......Page 64
Objects, Metadata, and Serialization......Page 67
A Simple Solution Using Tags (Keywords)......Page 68
An Object-oriented Design......Page 69
A Better Solution Using Meta-objects......Page 79
Medical Images: Incorporating Binary Data......Page 86
XML......Page 91
Database Systems and Ideas......Page 98
The Relational Model......Page 99
The Entity--Attribute--Value Model......Page 106
Data Quality......Page 107
Data, Information and Knowledge......Page 109
Summary......Page 111
2 Symbolic Biomedical Knowledge......Page 112
A World Class Reasoning Example......Page 114
Symbolic Theories......Page 115
Logic and Inference Systems......Page 118
Predicate Calculus......Page 119
Unsound Inference: Abduction and Induction......Page 137
First Order Logic......Page 138
Rule-based Programming for FOL......Page 146
Limitations of FOL......Page 152
Frames, Semantic Nets, and Ontologies......Page 155
A Simple Frame System......Page 156
Extensions to Frame Systems......Page 172
Frames and Object-oriented Programming Languages......Page 175
Description Logics......Page 176
Description Logic Languages......Page 179
Examples from GALEN......Page 180
The Semantic Web......Page 183
Search......Page 186
A General Framework for Search......Page 187
Uninformed Search Strategies......Page 191
Informed Search Strategies......Page 193
Path Search......Page 195
Summary......Page 196
3 Probabilistic Biomedical Knowledge......Page 198
Probability......Page 199
Statistics......Page 200
The Laws of Probability......Page 201
Conditional Probability......Page 203
Independence......Page 204
Random Variables and Estimation......Page 205
Application and Generalization of Bayes' Rule......Page 212
Simple Bayesian Inference......Page 214
Non-Boolean Variables......Page 215
Bayes Nets......Page 216
Utility and Decision Modeling......Page 220
A Decision Analysis Vignette......Page 221
Graph Structure and Probability Assignment......Page 222
Determining Utilities......Page 223
Computation of Expected Values......Page 224
Encoding of Messages......Page 226
Entropy and Information......Page 229
Efficient Encoding......Page 230
Information Theory in Biology and Medicine......Page 233
Summary......Page 234
Information Retrieval Systems......Page 235
Indexing......Page 239
Processing Queries......Page 244
Ranking the Results......Page 245
Performance Evaluation......Page 246
Network Access to Document Repositories......Page 247
Natural Language Processing......Page 258
Biomedical Images......Page 260
Summary......Page 262
II Biomedical Ideas and Computational Realizations......Page 263
5 Computing With Genes, Proteins, and Cells......Page 265
Getting Data From Files......Page 267
Computing With DNA Sequences......Page 271
Mapping Genes to Proteins......Page 276
Representing Amino Acid and Proteins......Page 280
Simple Properties of Proteins From Sequence Data......Page 283
Amino Acid Profiles......Page 284
The Gene Ontology......Page 289
Biochemical Pathways......Page 292
Searching for Pathways......Page 293
Biochemical Reachability Logic......Page 299
Simulation With State Machines......Page 302
State Machines......Page 303
A Simple State Machine......Page 305
Simulating the Cell Cycle in Yeast......Page 309
Summary......Page 314
6 Modeling Biological Structure......Page 315
The Components of the FMA......Page 316
Metaclasses......Page 317
A Simple Network Interface -- the FMS......Page 320
Semantic Consistency Checking and the FMA......Page 327
The Lymphatic System: An Example......Page 329
Current State of the Lymphatics in the FMA......Page 331
Summary......Page 334
7 Drug Interactions......Page 336
Drug Information Catalogs......Page 338
Reasoning About Pharmacokinetics......Page 342
Procedural Knowledge About Enzymatic Metabolism......Page 344
A Rule-based Drug Interaction System......Page 345
Truth Maintenance Systems......Page 348
A Drug Interactions Theory with Justifications......Page 351
Evidence-based Reasoning......Page 353
Reasoning About Pharmacodynamics......Page 355
Summary......Page 358
8 Medical Data Communication......Page 359
EMR Systems......Page 360
Network Architecture......Page 362
Network Client and Server Design......Page 364
The HL7 Message Exchange Protocol......Page 366
HL7 Message Structure......Page 367
Scanning HL7 Messages......Page 369
HL7 Message Field Content......Page 371
A Short History of DICOM......Page 374
About the DICOM Standard......Page 376
How to Implement DICOM......Page 380
The DICOM State Machine......Page 381
Parsing and Generation of PDUs......Page 390
Parsing and Generation of Commands and Data......Page 396
How It All Turned Out......Page 400
Summary......Page 401
9 Cancer Radiotherapy Planning......Page 402
Radiation Therapy......Page 403
Radiotherapy Planning Software......Page 404
Locating the Target......Page 407
Computing the CTV......Page 409
Computing the PTV......Page 415
Influence Diagrams in RTP......Page 422
Summary......Page 423
A Bit of Personal History and Perspective......Page 425
Some Real-Life Stories......Page 427
Radiation Therapy Planning Systems......Page 428
The Therac-25: A Real-Time Disaster......Page 430
The UW Neutron Therapy Facility......Page 431
Intravenous Infusion Pumps on the Internet......Page 432
Safety By Design: Radiotherapy Machines......Page 433
A Simple Linac Control System......Page 434
Adding a Dosimetry System......Page 436
It Security in Health Care Organizations......Page 437
Epilogue......Page 439
General Notes on Lisp......Page 441
CLOS and MOP......Page 442
Optimization......Page 444
Books on Lisp......Page 445
Data and Knowledge Resources......Page 446
Languages and Tools for Knowledge Representation......Page 447
Other Resources......Page 448
Bibliography......Page 451
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