METHODS IN MEDICAL INFORMATICS

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1 Chapman & Hall/CRC Mathematical and Computational Biology Series METHODS IN MEDICAL INFORMATICS Fundamentals of Healthcare Programming in Perln Pythoni and Ruby Jules J- Berman TECHNISCHE INFORMATION SBIBLIOTHEK UNIVERSITATSBIBLIOTHEK HANNOVER V J CRC Press Taylor & Francis Group Boca Raton London NewYork CRC Press is an imprint of the Taylor & Francis Group an Informa business A CHAPMAN & HALL BOOK

2 Contents Preface Nota Bene About the Author xv xxi xxiii Part I Fundamental Algorithms and Methods of Medical Informatics Chapter 1 Parsing and Transforming Text Files Peeking into Large Files Analysis Paging through Large Text Files Analysis Extracting Lines that Match a Regular Expression Analysis Changing Every File in a Subdirectory Analysis Counting the Words in a File Analysis Making a Word List with Occurrence Tally Analysis Using Printf Formatting Style Analysis 18 VII

3 VIII CONTENTS Chapter 2 Utility Scripts Random Numbers Analysis Converting Non-ASCII to Base64 ASCII Analysis Creating a Universally Unique Identifier Analysis Splitting Text into Sentences Analysis One-Way Hash on a Name Analysis One-Way Hash on a File Analysis A Prime Number Generator Analysis 34 Chapter 3 Viewing and Modifying Images Viewing a JPEG Image Analysis Converting between Image Formats Analysis Batch Conversions Analysis Drawing a Graph from List Data Analysis Drawing an Image Mashup Analysis 50 Chapter 4 Indexing Text ZIPF Distribution of a Text File Analysis a Preparing Concordance Analysis Extracting Phrases Analysis Preparing an Index Analysis 68

4 CONTENTS IX 4.5 Comparing Texts Using Similarity Scores Analysis 76 Part II Medical Data Resources Chapter 5 The National Library of Medicine's Medical Subject Headings (MeSH) Determining the Hierarchical Lineage for MeSH Terms Analysis a Creating MeSH Database Analysis Reading the MeSH Database Analysis Creating an SQLite Database for MeSH Analysis Reading the SQLite MeSH Database Analysis 97 Chapter 6 The International Classification of Diseases Creating the ICD Dictionary Analysis Building the ICD-O (Oncology) Dictionary Analysis 104 Chapter 7 SEER: The Cancer Surveillance, Epidemiology, and End Results Program Parsing the SEER Data Files Analysis Finding the Occurrences ofall Cancers in the SEER Data Files Analysis Finding the Age Distributions of the Cancers in the SEER Data Files Analysis 119 Chapter 8 OMIM: The Online Mendehan Inheritance in Man Collecting the OMIM Entry Terms Analysis Finding Inherited Cancer Conditions Analysis 128

5 X CONTENTS Chapter 9 PubMed Building a Large Text Corpus of Biomedical Information Analysis Creating a List of Doublets from a PubMed Corpus Analysis Downloading Gene Synonyms from PubMed Downloading Protein Synonyms from PubMed 140 Chapter 10 Taxonomy Finding Taxonomic 143 Hierarchy a Analysis Finding the Restricted Classes ofhuman Infectious Pathogens Analysis 153 Chapter 11 Developmental Lineage Classification and Taxonomy of Neoplasms Building the Doublet Hash Analysis 11.2 Scanning the Literature for Candidate Terms Analysis Adding Terms to the Neoplasm Classification Analysis 11.4 Determining the Lineage of Every Neoplasm Concept Analysis Chapter 12 U.S. Census Files Total Population of the United States Analysis 12.2 Stratified Distribution for the U.S. Census Analysis Adjusting for Age Analysis Chapter 13 Centers for Disease Control and Prevention Mortality Files Death Certificate Data Obtaining the CDC Data Files How Death Certificates Are Represented in Data Records Ranking, by Number of Occurrences, Every Condition in the CDC Mortality Files Analysis 204

6 CONTENTS XI Part III Primary Tasks of Medical Informatics Chapter 14 Autocoding A Neoplasm Autocoder Analysis Recoding 216 Chapter 15 Text Scrubber for Deidentifying Confidential Text Analysis 222 Chapter 16 Web Pages and CGI Scripts Grabbing Web 227 Pages Analysis CGI Script for Searching the Neoplasm Classification Analysis 235 Chapter 17 Image Annotation a Inserting Header Comment Analysis Extracting the Header Comment in a JPEG Image File Analysis Inserting IPTC Annotations Extracting Comment, EXIF, and IPTC Annotations Analysis Dealing with DICOM Finding DICOM Images DICOM-to-JPEG Conversion Analysis 246 Chapter 18 Describing Data with Data, Using XML Parsing XML Analysis Resource Description Framework (RDF) Dublin Core Metadata Insert an RDF Document into an Image File Analysis Insert an Image File into an RDF Document Analysis RDF Schema Visualizing an RDF Schema with GraphViz Obtaining GraphViz 262

7 XII CONTENTS 18.8 Converting a Data Structure to GraphViz Analysis 265 Part IV Medical Discovery Chapter 19 Case Study: Emphysema Rates Analysis 273 Chapter 20 Case Study: Cancer Occurrence Rates Analysis 281 Chapter 21 Case Study: Germ Cell Tumor Rates across Ethnicities Analysis 293 Chapter 22 Case Study: Ranking the Death-Certifying Process, by State Analysis 298 Chapter 23 Case Study: Data Mashups for Epidemics Tally of Coccidioidomycosis Cases by State Analysis Creating the Map Mashup Analysis 311 Chapter 24 Case Study: Sickle Cell Rates Analysis 318 Chapter 25 Case Study: Site-Specific Tumor Biology Anatomic Origins of Mesotheliomas Mesothelioma Records in the SEER Data Sets Analysis Graphic Representation Analysis 333 Chapter 26 Case Study: Bimodal Tumors Analysis 344 Chapter 27 Case Study: The Age of Occurrence of Precancers Analysis 357

8 CONTENTS XIII Epilogue for Healthcare Professionals and Medical Scientists 361 Learn One or More Open Source Programming Languages 361 Don't Agonize Over Which Language You Should Choose 362 Learn Algorithms 362 Unless You Are a Professional Programmer, Relax and a Enjoy Being Newbie 363 Do Not Delegate Simple Programming Tasks to Others 363 Break Complex Tasks into Simple Methods and Algorithms 364 Write Fast Scripts 364 Concentrate on the Questions, Not the Answers 365 Appendix 367 How to Acquire Ruby 367 How to Acquire Perl 367 How to Acquire Python 367 How to Acquire RMagick 368 How to Acquire SQLite 369 How to Acquire the Public Data Files Used in This Book 370 Other Publicly Available Files, Data Sets, and Utilities 376 Index 377

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