Methods in Medical Informatics: Fundamentals of Healthcare Programming in Perl, Python, and Ruby (Chapman & Hall CRC Mathematical & Computational Biology)

401 Pages·2010·5.86 MB·English

by  Jules J. Berman

METHODS IN MEDICAL INFORMATICS
Fundamentals of Healthcare Programming
in Perl, Python, and Ruby
CHAPMAN & HALL/CRC
Mathematical and Computational Biology Series
Aims and scope:
This series aims to capture new developments and summarize what is known
over the entire spectrum of mathematical and computational biology and
medicine. It seeks to encourage the integration of mathematical, statistical,
and computational methods into biology by publishing a broad range of
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series are meant to appeal to students, researchers, and professionals in the
mathematical, statistical and computational sciences, fundamental biology
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field. The inclusion of concrete examples and applications, and programming
techniques and examples, is highly encouraged.
Series Editors
N. F. Britton
Department of Mathematical Sciences
University of Bath
Xihong Lin
Department of Biostatistics
Harvard University
Hershel M. Safer
Maria Victoria Schneider
European Bioinformatics Institute
Mona Singh
Department of Computer Science
Princeton University
Anna Tramontano
Department of Biochemical Sciences
University of Rome La Sapienza
Proposals for the series should be submitted to one of the series editors above or directly to:
CRC Press, Taylor & Francis Group
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METHODS IN MEDICAL INFORMATICS
Fundamentals of Healthcare Programming
in Perl, Python, and Ruby
Jules J. Berman
Chapman & Hall/CRC
Taylor & Francis Group
6000 Broken Sound Parkway NW, Suite 300
Boca Raton, FL 33487-2742
© 2011 by Taylor and Francis Group, LLC
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Library of Congress Cataloging-in-Publication Data
Berman, Jules J.
Methods in medical informatics : fundamentals of healthcare programming in Perl, Python, and Ruby /
Jules J. Berman.
p. ; cm. -- (Chapman & Hall/CRC mathematical and computational biology series ; 39)
Includes bibliographical references and index.
ISBN 978-1-4398-4182-2 (alk. paper)
1. Medical informatics--Methodology. 2. Medicine--Data processing. I. Title. II. Series: Chapman and
Hall/CRC mathematical & computational biology series ; 39.
[DNLM: 1. Medical Informatics--methods. 2. Programming Languages. 3. Computing Methodologies.
W 26.5 B516m 2011]
R858.B4719 2011
610.285--dc22 2010011244
Visit the Taylor & Francis Web site at
http://www.taylorandfrancis.com
and the CRC Press Web site at
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For Irene

Contents
Preface x v
Nota BeNe xxi
aBout the author xxiii
Part I fuNdameNtal algorIthms aNd methods
of medIcal INformatIcs
chaPter 1 ParsINg aNd traNsformINg text fIles 3
1.1 Peeking into Large Files 3
1.1.1 Script Algorithm 3
1.1.2 Analysis 5
1.2 Paging through Large Text Files 5
1.2.1 Script Algorithm 5
1.2.2 Analysis 7
1.3 Extracting Lines that Match a Regular Expression 7
1.3.1 Script Algorithm 8
1.3.2 Analysis 1 0
1.4 Changing Every File in a Subdirectory 1 0
1.4.1 Script Algorithm 1 0
1.4.2 Analysis 1 1
1.5 Counting the Words in a File 1 2
1.5.1 Script Algorithm 12
1.5.2 Analysis 1 4
1.6 Making a Word List with Occurrence Tally 1 4
1.6.1 Script Algorithm 1 4
1.6.2 Analysis 1 6
1.7 Using Printf Formatting Style 1 6
1.7.1 Script Algorithm 1 7
1.7.2 Analysis 18
vii
viii Contents
chaPter 2 utIlIty scrIPts 2 1
2.1 Random Numbers 2 1
2.1.1 Script Algorithm 2 1
2.1.2 Analysis 2 2
2.2 Converting Non-ASCII to Base64 ASCII 2 2
2.2.1 Script Algorithm 2 3
2.2.2 Analysis 2 4
2.3 Creating a Universally Unique Identifier 2 4
2.3.1 Script Algorithm 24
2.3.2 Analysis 2 5
2.4 Splitting Text into Sentences 2 5
2.4.1 Script Algorithm 26
2.4.2 Analysis 26
2.5 One-Way Hash on a Name 2 7
2.5.1 Script Algorithm 2 8
2.5.2 Analysis 3 0
2.6 One-Way Hash on a File 3 0
2.6.1 Script Algorithm 3 0
2.6.2 Analysis 3 1
2.7 A Prime Number Generator 3 1
2.7.1 Script Algorithm 3 2
2.7.2 Analysis 3 4
chaPter 3 VIewINg aNd modIfyINg Images 3 7
3.1 Viewing a JPEG Image 3 7
3.1.1 Script Algorithm 38
3.1.2 Analysis 3 9
3.2 Converting between Image Formats 4 0
3.2.1 Script Algorithm 4 0
3.2.2 Analysis 4 1
3.3 Batch Conversions 4 2
3.3.1 Script Algorithm 4 2
3.3.2 Analysis 4 3
3.4 Drawing a Graph from List Data 4 4
3.4.1 Script Algorithm 4 4
3.4.2 Analysis 4 6
3.5 Drawing an Image Mashup 4 6
3.5.1 Script Algorithm 4 6
3.5.2 Analysis 5 0
chaPter 4 INdexINg text 5 3
4.1 ZIPF Distribution of a Text File 53
4.1.1 Script Algorithm 5 4
4.1.2 Analysis 5 6
4.2 Preparing a Concordance 5 7
4.2.1 Script Algorithm 5 7
4.2.2 Analysis 5 9
4.3 Extracting Phrases 6 0
4.3.1 Script Algorithm 6 1
4.3.2 Analysis 6 3
4.4 Preparing an Index 6 3
4.4.1 Script Algorithm 6 5
4.4.2 Analysis 6 8
Contents ix
4.5 Comparing Texts Using Similarity Scores 6 9
4.5.1 Script Algorithm 6 9
4.5.2 Analysis 7 6
Part II medIcal data resources
chaPter 5 the NatIoNal lIBrary of medIcINe’s medIcal suBject
headINgs (mesh) 8 1
5.1 Determining the Hierarchical Lineage for MeSH Terms 8 3
5.1.1 Script Algorithm 8 3
5.1.2 Analysis 8 6
5.2 Creating a MeSH Database 8 8
5.2.1 Script Algorithm 8 8
5.2.2 Analysis 90
5.3 Reading the MeSH Database 9 0
5.3.1 Script Algorithm 9 1
5.3.2 Analysis 9 2
5.4 Creating an SQLite Database for MeSH 9 2
5.4.1 Script Algorithm 9 3
5.4.2 Analysis 9 6
5.5 Reading the SQLite MeSH Database 9 6
5.5.1 Script Algorithm 9 6
5.5.2 Analysis 9 7
chaPter 6 the INterNatIoNal classIfIcatIoN of dIseases 9 9
6.1 Creating the ICD Dictionary 9 9
6.1.1 Script Algorithm 100
6.1.2 Analysis 101
6.2 Building the ICD-O (Oncology) Dictionary 102
6.2.1 Script Algorithm 103
6.2.2 Analysis 104
chaPter 7 seer: the caNcer surVeIllaNce, ePIdemIology, aNd
eNd results Program 107
7.1 Parsing the SEER Data Files 107
7.1.1 Script Algorithm 107
7.1.2 Analysis 109
7.2 Finding the Occurrences of All Cancers in the SEER Data Files 110
7.2.1 Script Algorithm 111
7.2.2 Analysis 114
7.3 Finding the Age Distributions of the Cancers in the SEER Data Files 115
7.3.1 Script Algorithm 115
7.3.2 Analysis 119
chaPter 8 omIm: the oNlINe meNdelIaN INherItaNce IN maN 123
8.1 Collecting the OMIM Entry Terms 124
8.1.1 Script Algorithm 124
8.1.2 Analysis 125
8.2 Finding Inherited Cancer Conditions 126
8.2.1 Script Algorithm 126
8.2.2 Analysis 128