Methods in Medical Informatics: Fundamentals of Healthcare Programming in Perl, Python, and Ruby / Edition 1

by Jules J. Berman

Overview

Too often, healthcare workers are led to believe that medical informatics is a complex field that can only be mastered by teams of professional programmers. This is simply not the case. With just a few dozen simple algorithms, easily implemented with open source programming languages, you can fully utilize the medical information contained in clinical and research datasets. The common computational tasks of medical informatics are accessible to anyone willing to learn the basics.

Methods in Medical Informatics: Fundamentals of Healthcare Programming in Perl, Python, and Ruby demonstrates that biomedical professionals with fundamental programming knowledge can master any kind of data collection. Providing you with access to data, nomenclatures, and programming scripts and languages that are all free and publicly available, this book —

• Describes the structure of data sources used, with instructions for downloading
• Includes a clearly written explanation of each algorithm
• Offers equivalent scripts in Perl, Python, and Ruby, for each algorithm
• Shows how to write short, quickly learned scripts, using a minimal selection of commands
• Teaches basic informatics methods for retrieving, organizing, merging, and analyzing data sources
• Provides case studies that detail the kinds of questions that biomedical scientists can ask and answer with public data and an open source programming language

Requiring no more than a working knowledge of Perl, Python, or Ruby, Methods in Medical Informatics will have you writing powerful programs in just a few minutes. Within its chapters, you will find descriptions of the basic methods and implementations needed to complete many of the projects you will encounter in your biomedical career.

Product Details

ISBN-13:	9781439841822
Publisher:	Taylor & Francis
Publication date:	09/22/2010
Series:	Chapman & Hall/CRC Computational Biology Series , #39
Edition description:	New Edition
Pages:	416
Product dimensions:	7.00(w) x 10.10(h) x 1.10(d)

About the Author

Jules Berman, Ph.D., M.D., received two bachelor of science degrees (mathematics and earth sciences) from MIT, a Ph.D. in pathology from Temple University, and an M.D. from the University of Miami School of Medicine. His postdoctoral research was conducted at the National Cancer Institute. His medical residence in pathology was completed at the George Washington University School of Medicine. He became board certified in anatomic pathology and in cytopathology, and served as the chief of Anatomic Pathology, Surgical Pathology and Cytopathology at the Veterans Administration (VA) Medical Center in Baltimore, Maryland.

While at the Baltimore VA, Dr. Berman held appointments at the University of Maryland Medical Center and at theJohns Hopkins Medical Institutions. In 1998, he became the program director for pathology informatics in the Cancer Diagnosis Program at the U.S. National Cancer Institute. In 2006, he became president of the Association for Pathology Informatics. Over the course of his career, he has written, as first author, more than 100 publications, including five books in the field of medical informatics. Today, Dr. Berman is a full-time freelance writer.

Table of Contents

FUNDAMENTAL ALGORITHMS AND METHODS OF MEDICAL INFORMATICS: Parsing and Transforming Text Files. Utility Scripts. Viewing and Modifying Images. MEDICAL DATA RESOURCES: The National Library of Medicine’s Medical Subject Headings (MeSH ). The International Classification of Diseases. SEER: The Cancer Surveillance, Epidemiology, and End Results Program. OMIM: The Online Mendelian Inheritance in Man. PubMed. Taxonomy. Developmental Lineage Classification and Taxonomyof Neoplasms. U.S. Census Files. Centers for Disease Control and Prevention Mortality Files. PRIMARY TASKS OF MEDICAL INFORMATICS: Autocoding. Text Scrubber for Deidentifyin g Confidential Text. Web Pages and CGI Scripts. Image Annotation. Describing Data with Data, Using XML. MEDICAL DISCOVERY: Case Study: Emphysema Rates. Case Study: Cancer Occurrence Rates. Case Study: Germ Cell Tumor Rates across Ethnicities. Case Study: Ranking the Death-Certifying Process, by State. Case Study: Data Mashups for Epidemics. Case Study: Sickle Cell Rates. Case Study: Site-Specific Tumor Biology. Case Study: Bimodal Tumors. Case Study: The Age of Occurrence of Precancers. . Appendix. How to Acquire Ruby. How to Acquire Perl. How to Acquire Python. How to Acquire RMagick. How to Acquire SQLite. How to Acquire the Public Data Files Used in This Book. Other Publicly Available Files, Data Sets, and Utilities.

What People are Saying About This

From the Publisher

As subspecialty board certification in clinical informatics has finally become a reality, Jules Berman’s Methods in Medical Informatics could not be more timely. This well-written and informative text combines Dr. Berman’s expertise in programming with his vast knowledge of publicly available data sets and everyday healthcare programming needs to result in a book which … should become a staple in health informatics education programs as well as a standard addition to the personal libraries of informaticists.
—Alexis B. Carter, Journal of Pathology Informatics, October 2011

This book provides an introduction to processing clinical and population health data using rigorous methods and widely available, low cost, but very capable tools. The inclusion of the three leading dynamic programming languages broadens the appeal … bridges the gap from programming instruction to dealing with specialized medical data, making it possible to teach a relevant programming course in a biomedical environment. I would have loved to have a copy of this when I was teaching introductory programming for medical informatics.
—Professor James H. Harrison, Jr., Director of Clinical Informatics, University of Virginia

… presents students and professionals in the healthcare field (who have some working knowledge of the open-source programming languages Perl, Python, or Ruby) with instruction for applying basic informatics algorithms to medical data sets. He [the author] provides algorithm scripts for each of the languages, along with step-by-step explanations of the algorithms used for retrieving, organizing, merging, and analyzing such data sources as the National Cancer Institute’s Surveillance Epidemiology and End Results project, the National Library of Medicine’s PubMed service, the mortality records of the US Centers for Disease Control and Prevention, the US Census, and the Online Mendelian Inheritance in Man data set on inherited conditions.
—SciTech Book News, February 2011

Editorial Reviews

Reviewer: Frank R Ames, Ph.D.(Rocky Vista University College of Osteopathic Medicine)
Description: Innovative and sophisticated analyses of medical data do not require commercial software or professional programming. Healthcare workers who possess rudimentary programming skills can use open source programming languages and simple algorithms to mine, analyze, and present information found in electronic health records, biomedical data sets, and medical literature databases. This book shows how.
Purpose: It presents model scripts, step-by-step instructions, and case studies that show nonspecialists how to write computer programs to mine data for research projects. Healthcare professionals who are not professional programmers need to know how to extract medical information, and the book meets this need.
Audience: Designed for students and professionals in healthcare, the book functions as a textbook and a handbook. Readers must understand the basics of programming and have a working knowledge of the Perl, Python, and Ruby programming languages, but they need not be experts to benefit from this book, which is designed for novices and written by an expert, Jules Berman, a former president of the Association for Pathology Informatics.
Features: The book presents algorithms for parsing, transforming, and indexing text files; discusses public data sources such as the NLM's Medical Subject Headings, U.S. Census Files, and CDC Mortality Files; explains auto coding, text scrubbing, and similar tasks; presents case studies on rates of emphysema and other diseases; and concludes with practical advice and directions for acquiring programming languages and public data. Readers will appreciate that the programming languages and data used are available at no cost and are either in the public domain or are distributed under a general public license. The structure of data sets is described; programming scripts are short and focused; equivalent scripts for each algorithm are given in three programming languages (Perl, Python, and Ruby); step-by-step instructions, clear explanations, relevant exercises, and realistic case studies show how scripts are used; and additional resources, corrections, and updates are available online from the publisher's web site.
Assessment: This is a model book in basic informatics programming. The writing is simple, direct, and understandable; explanations are concise but complete; examples and case studies are apt and interesting; the advice is practical and grounded in significant experience and expertise. Unlike many programming guides, this one attends to the logic of the programming algorithms, not just the programming languages.

Doody's Review Service

As subspecialty board certification in clinical informatics has finally become a reality, Jules Berman’s Methods in Medical Informatics could not be more timely. This well-written and informative text combines Dr. Berman’s expertise in programming with his vast knowledge of publicly available data sets and everyday healthcare programming needs to result in a book which … should become a staple in health informatics education programs as well as a standard addition to the personal libraries of informaticists.
—Alexis B. Carter, Journal of Pathology Informatics, October 2011

This book provides an introduction to processing clinical and population health data using rigorous methods and widely available, low cost, but very capable tools. The inclusion of the three leading dynamic programming languages broadens the appeal … bridges the gap from programming instruction to dealing with specialized medical data, making it possible to teach a relevant programming course in a biomedical environment. I would have loved to have a copy of this when I was teaching introductory programming for medical informatics.
—Professor James H. Harrison, Jr., Director of Clinical Informatics, University of Virginia

… presents students and professionals in the healthcare field (who have some working knowledge of the open-source programming languages Perl, Python, or Ruby) with instruction for applying basic informatics algorithms to medical data sets. He [the author] provides algorithm scripts for each of the languages, along with step-by-step explanations of the algorithms used for retrieving, organizing, merging, and analyzing such data sources as the National Cancer Institute’s Surveillance Epidemiology and End Results project, the National Library of Medicine’s PubMed service, the mortality records of the US Centers for Disease Control and Prevention, the US Census, and the Online Mendelian Inheritance in Man data set on inherited conditions.
—SciTech Book News, February 2011

From the Publisher