Principles of biomedical informatics:
Saved in:
| Main Author: | |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Amsterdam [u.a.]
Elsevier, Acad. Press
2009
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| Edition: | 1. ed. |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XXV, 475 S. Ill. |
| ISBN: | 9780123694386 0123694388 |
Staff View
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| 100 | 1 | |a Kalet, Ira J. |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a Principles of biomedical informatics |c Ira J. Kalet |
| 246 | 1 | 3 | |a Biomedical informatics |
| 250 | |a 1. ed. | ||
| 264 | 1 | |a Amsterdam [u.a.] |b Elsevier, Acad. Press |c 2009 | |
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| 650 | 4 | |a Medical informatics | |
| 650 | 4 | |a Bioinformatics | |
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Record in the Search Index
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|---|---|
| adam_text | Foreword xiii
Preface xvii
Parti
Foundations of Biomedical Informatics
1 Biomedical Data 3
1.1 The Nature and Representation of Biomedical Data 6
1.1.1 What Can Be Represented in a Computer? 13
1.1.2 DNA and the Genetic Code 27
1.1.3 Anatomy 37
1.1.4 Medical Laboratory Data 38
1.1.5 Medical Images 42
1.1.6 Metadata 50
1.2 Objects, Metadata, and Serialization 53
1.2.1 A Simple Solution Using Tags (Keywords) 54
1.2.2 An Object-oriented Design 55
1.2.3 A Better Solution Using Meta-objects 65
1.2.4 Medical Images: Incorporating Binary Data 72
1.3 XML 77
1.4 Database Systems and Ideas 84
1.4.1 The Relational Model 85
1.4.2 The Entity-Attribute-Value Model 92
1.5 Data Quality 93
1.6 Data, Information, and Knowledge 95
1.7 Summary 97
2 Symbolic Biomedical Knowledge 99
2.1 Biomedical Theories and Computer Programs 101
2.1.1 A World Class Reasoning Example 101
2.1.2 Biological Examples 102
2.1.3 Symbolic Theories 102
vii
2.2 Logic and Inference Systems 105
2.2.1 Predicate Calculus 106
2.2.2 Unsound Inference: Abduction and Induction 124
2.2.3 First Order Logic 125
2.2.4 Rule-based Programming for FOL 133
2.2.5 Limitations of FOL 139
2.3 Frames, Semantic Nets, and Ontologies 142
2.3.1 A Simple Frame System 143
2.3.2 Extensions to Frame Systems 159
2.3.3 Frame System Implementations, Interfaces, and APIs 162
2.3.4 Frames and Object-oriented Programming Languages 162
2.4 Description Logics 163
2.4.1 Description Logic Languages 166
2.4.2 Examples from GALEN 167
2.4.3 The Semantic Web 170
2.4.4 Back to the Future 173
2.5 Search 173
2.5.1 A General Framework for Search 174
2.5.2 Uninformed Search Strategies 178
2.5.3 Informed Search Strategies 180
2.5.4 Path Search 182
2.6 Summary 183
3 Probabilistic Biomedical Knowledge 185
3.1 Probability and Statistics 186
3.1.1 Probability 186
3.1.2 Statistics 187
3.1.3 The Laws of Probability 188
3.1.4 Conditional Probability 190
3.1.5 Independence 191
3.1.6 Random Variables and Estimation 192
3.2 Application and Generalization of Bayes Rule 199
3.2.1 Simple Bayesian Inference 201
3.2.2 Non-Boolean Variables 202
3.2.3 Bayes Nets 203
3.3 Utility and Decision Modeling 207
3.3.1 A Decision Analysis Vignette 208
3.3.2 Graph Structure and Probability Assignment 209
3.3.3 Determining Utilities 210
3.3.4 Computation of Expected Val ues 211
3.4 Information Theory 213
3.4.1 Encoding of Messages 213
3.4.2 Entropy and Information 216
3.4.3 Efficient Encoding 217
3.4.4 Error Detection and Correction 220
3.4.5 information Theory in Biology and Medicine 220
3.5 Summary 221
4 Biomedical Information Access 223
4.1 Information Retrieval Systems 223
4.2 IR System Design 227
4.2.1 Indexing 227
4.2.2 Processing Queries 232
4.2.3 Searching and Matching 233
4.2.4 Ranking the Results 233
4.2.5 Performance Evaluation 234
4.3 Intelligent Query Processing 235
4.4 Network Access to Document Repositories 235
4.5 Natural Language Processing 246
4.6 Beyond Text Documents 248
4.6.1 Biomedical Images 249
4.6.2 Electronic Medical Records 250
4.7 Summary 250
Part II
Biomedical Ideas and Computational Realizations
5 Computing With Genes, Proteins, and Cells 253
5.1 Getting Data from Files 255
5.2 Computing With DNA Sequences 259
5.3 Mapping Genes to Proteins 264
5.4 Computing With Protein Sequences 268
5.4.1 Representing Amino Acid and Proteins 268
5.4.2 Simple Properties of Proteins from Sequence Data 271
5.4.3 Amino Acid Profiles 272
5.5 The Gene Ontology 277
5.6 Biochemical Pathways 280
5.6.1 Searching for Pathways 281
5.6.2 Biochemical Reachability Logic 287
5.7 Simulation With State Machines 291
5.7.1 State Machines 291
5.7.2 A Simple State Machine 293
5.7.3 Simulating the Cell Cycle in Yeast 297
5.8 Summary 302
6 Modeling Biological Structure 303
6.1 The UW Foundational Model of Anatomy 304
6.1.1 The Components of the FMA 304
6.1.2 Representing Anatomical Relations in the FMA 305
6.1.3 Metaclasses 305
6.1.4 The paxt-of Relationship 308
6.2 A Simple Network Interface-the FMS 308
I
6.3 Semantic Consistency Checking and the FMA 315
6.3.1 The Lymphatic System: An Example 317
6.3.2 Current State of the Lymphatics in the FMA 319
6.4 Summary 323
7 Drug Interactions 325
7.1 Drug Information Catalogs 327
7.2 Reasoning About Pharmacokinetics 331
7.2.1 Procedural Knowledge About Enzymatic Metabolism 333
7.2.2 A Rule-based Drug Interaction System 334
7.2.3 Truth Maintenance Systems 337
7.2.4 A Drug Interactions Theory with (ustifications 340
7.2.5 Evidence-based Reasoning 342
7.3 Reasoning About Pharmacodynamics 345
7.4 Summary 347
8 Medical Data Communication 349
8.1 EMR Systems and PACS 350
8.1.1 EMR Systems 350
8.1.2 Medical Images and PACS 352
8.2 Networks and Protocols 352
8.2.1 Network Architecture 352
8.2.2 Network Client and Server Design 354
8.3 HL7 356
8.3.1 The HL7 Message Exchange Protocol 356
8.3.2 HL7 Message Structure 357
8.3.3 Scanning HL7 Messages 359
8.3.4 HL7 Message Field Content 361
8.4 DICOM: Medical Image Information Agents 364
8.4.1 A Short History of DICOM 364
8.4.2 About the DICOM Standard 366
8.5 How to Implement DICOM 370
8.5.1 The DICOM State Machine 371
8.5.2 Parsing and Generation of PDUs 380
8.5.3 Parsing and Generation of Commands and Data 386
8.5.4 How It All Turned Out 390
8.6 Summary 391
9 Cancer Radiotherapy Planning 393
9.1 Radiation Therapy 394
9.2 Radiotherapy Planning Software 395
9.3 Locating the Target 398
9.3.1 Computing the CTV 400
9.3.2 Computing the PTV 406
9.4 Influence Diagrams in RTP 413
9.5 Summary 414
10 Safety and Security 411
10.1 A Bit of Personal History and Perspective 418
10.2 Some Reai-Life Stories 419
10.2.1 Radiation Therapy Planning Systems 420
10.2.2 Who is Master, the Human or the Computer? 422
10.2.3 The Therac-25: A Real-Time Disaster 422
10.2.4 Prism 423
10.2.5 The UW Neutron Therapy Facility 423
10.2.6 DICOM and Internet Security 424
10.2.7 Intravenous Infusion Pumps on the Internet 424
10.3 Safety by Design: Radiotherapy Machines 425
10.3.1 A Simple Linac Control System 426
10.3.2 Adding a Dosimetry System 428
10.3.3 Formal and Automated Analysis 429
10.4 IT Security in Health Care Organizations 429
10.5 Epilogue 431
Appendix
A Lisp Notes, Software, and Other Resources 433
A.I Lisp Notes 433
A. 1.1 General Notes on Lisp 433
A. 1.2 CLOSandMOP 434
A. 1.3 Optimization 436
A. 1.4 Books on Lisp 437
A.2 Software 438
A.2.1 Data and Knowledge Resources 438
A.2.2 Common Lisp Systems, Libraries, and Resources 439
A.2.3 Languages and Tools for Knowledge Representation 439
A. 2.4 Code from the Book 440
A.3 Other Resources 441
Bibliography 443
Index 459
|
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| author | Kalet, Ira J. |
| author_facet | Kalet, Ira J. |
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| dewey-search | 610.28 |
| dewey-sort | 3610.28 |
| dewey-tens | 610 - Medicine and health |
| discipline | Biologie Informatik Medizin |
| edition | 1. ed. |
| format | Book |
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| indexdate | 2024-07-09T21:31:51Z |
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| isbn | 9780123694386 0123694388 |
| language | English |
| lccn | 2008030982 |
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| physical | XXV, 475 S. Ill. |
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| spelling | Kalet, Ira J. Verfasser aut Principles of biomedical informatics Ira J. Kalet Biomedical informatics 1. ed. Amsterdam [u.a.] Elsevier, Acad. Press 2009 XXV, 475 S. Ill. txt rdacontent n rdamedia nc rdacarrier Medical informatics Bioinformatics Medical Informatics Computational Biology Bioinformatik (DE-588)4611085-9 gnd rswk-swf Medizinische Informatik (DE-588)4038261-8 gnd rswk-swf Medizinische Informatik (DE-588)4038261-8 s DE-604 Bioinformatik (DE-588)4611085-9 s b DE-604 HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017152967&sequence=000004&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Kalet, Ira J. Principles of biomedical informatics Medical informatics Bioinformatics Medical Informatics Computational Biology Bioinformatik (DE-588)4611085-9 gnd Medizinische Informatik (DE-588)4038261-8 gnd |
| subject_GND | (DE-588)4611085-9 (DE-588)4038261-8 |
| title | Principles of biomedical informatics |
| title_alt | Biomedical informatics |
| title_auth | Principles of biomedical informatics |
| title_exact_search | Principles of biomedical informatics |
| title_full | Principles of biomedical informatics Ira J. Kalet |
| title_fullStr | Principles of biomedical informatics Ira J. Kalet |
| title_full_unstemmed | Principles of biomedical informatics Ira J. Kalet |
| title_short | Principles of biomedical informatics |
| title_sort | principles of biomedical informatics |
| topic | Medical informatics Bioinformatics Medical Informatics Computational Biology Bioinformatik (DE-588)4611085-9 gnd Medizinische Informatik (DE-588)4038261-8 gnd |
| topic_facet | Medical informatics Bioinformatics Medical Informatics Computational Biology Bioinformatik Medizinische Informatik |
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