Table of contents for Perl programming for medicine and biology / Jules J Berman.

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Perl Programming for Medicine and Biology
Jules J. Berman
Table of Contents
0. Preface.
0.1. Background.
0.2. Biomedical Computer Programming.
0.3. Choosing A Programming Language.
0.4. Biomedical Informatics, An Optional Companion Book Focused On Biomedical Data.
0.5. How To Read This Book.
0.6. Acknowledgments.
1. Introduction to Perl Programming.
1.1. Background.
1.2. Downloading And Installing Perl.
1.3. File Operations.
1.4. Perl Script Basics.
1.5. The Directory Path To Perl.
1.6. Do Not Panic! Perl Will Forgive You.
1.7. Pseudocode For A General Purpose Biomedical Program.
1.8. The Open1.pl Script, Line By Line.
1.9. An 8-line Perl Word Processor.
1.10. A Slightly Longer Command-line Text Editor.
1.11. A Subroutine That Generates Random File Names.
1.12. Interactively Reading Lines From A File.
1.13. Reading Through Large Files.
1.14. Getting Just What You Want With Perl Regular Expressions.
1.15. Pseudocode For Common Uses Of Regex (regular Expression Pattern Matching).
1.16. A Regex Example.
1.17. Regular Expression Modifiers And Examples.
1.18. Counting All The Words In A Text File.
1.19. Finding The Frequency Of Occurrence Of Each Word In A Text File (zipf Distribution).
1.20. A Perl Zipf Script.
1.21. The Zipf Script Introduces Perl Associative Arrays.
1.22. Formatting Output In The Zipf Script.
1.23. Creating A Persistent Database Object.
1.24. Retrieving Information From A Persistent Database Object.
1.25. Validating Xml Tags Using Regular Expressions.
1.26. Collecting Items Present On Each Of Two Lists (arrays).
1.27. Collecting Items Present On One List And Absent From Another.
1.28. What Have We Learned?
2. Using Perl Modules and Applying Some Fundamental Commands.
2.1. Background.
2.2. Sorting Big Files.
2.3. A Perl Module For Benchmarking.
2.4. A Perl Module For Timing Subroutines.
2.5. Approximate Word Matching With String::approx Module.
2.6. Creating A Word List.
3. File/Directory Operations and Text Transformations with Regular Expressions
3.1. Background.
3.2. Listing Files In A Directory With Readdir.
3.3. Listing Files In A Directory And Its Subdirectories With The File::list Module.
3.4. Concatenating Text Files.
3.5. More Perl Modules For File Operations.
3.6. Extracting Lines Of Text That Match A Regular Expression.
3.7. Ascii Characters.
3.8. Stripping Unprintable Ascii Characters Using Tr.
3.9. Converting Binary To Base64.
3.10. Nearly Justifying A Text File.
3.11. Preparing Ascii Files For Import To Word Processors.
3.12. Finding All The Medical Abbreviations In A File.
3.13. Filtering Negations.
3.14. Extracting An Email List From A Pubmed Search.
4. Indexing Text.
4.1. Background.
4.2. Concordance.
4.3. Indexes.
4.4. Automatic Term Extraction.
4.5. Bwt (burrows-wheeler Transform) Indexing.
5. Autocoding Biomedical Data with Nomenclatures.
5.1. Background.
5.2. Doublet Algorithm For A Fast Lexical Autocoder.
5.3. Automatic Expansion Of A Medical Nomenclature.
5.4. Extracting The Category 0 Vocabularies From Umls.
5.5. Collecting The Icd Codes From The Umls Metathesaurus.
6. Searching and Mining Data.
6.1. Background.
6.2. Searching Large Text Files.
6.3. Proximity Searching.
6.4. Finding Needles Fast Using A Binary-tree Search Of The Haystack.
6.5. On-the-fly Coded Data Retrieval Without Pre-coding.
7. Cryptography and Deidentification.
7.1. Background.
7.2. Perl Cryptography Modules.
7.3. One-way Hashing Algorithms.
7.4. One-way Hash Weaknesses: Dictionary Attacks And Collisions.
7.5. Computing A One-way Hash For A Word, Phrase Or File.
7.6. Threshold Protocol.
8. Scrubbing Data.
8.1. Background.
8.2. Scrubbing Text Using The Concept-match Method.
8.3. Composing A Large Corpus Of Medical Text.
8.4. Scrubbing Text Using The Doublet Method.
8.5. Creating A List Of Safe Doublets.
8.6. Removing Duplicate Items From A List File.
8.7. Warnings.
9. Finding and Exchanging Data Through the Worldwide Web.
9.1. Background.
9.2. Retrieving Information From The Internet.
9.3. Retrieving A File From The Web.
9.4. Rss Accumulators.
9.5. Cgi Scripts.
9.6. Sending And Receiving Post And Get Commands.
10. Creating, Parsing, and Transforming XML.
10.1. Background.
10.2. Xml Basics.
10.3. Collecting The Metadata Elements From Multiple Xml Files.
10.4. Converting Pod Text To An Indexed Html File.
10.5. Converting An Excel File To An Xml File Using Xml::excel.
10.6. Converting Xml Version Of Neocl.xml To The Flat-file Version.
11. Metadata, Ontologies, and the Meaning of Everything.
11.1. Background.
11.2. The Failure Of Xml.
11.3. The Value Of Rdf.
11.4. Statements Of Meaning.
11.5. Rdf Triples.
11.6. Extracting Triples From An Rdf Document.
11.7. Common Data Elements (cdes).
11.8. Iso-11179 Specification For Cdes.
11.9. Rdf Schemas.
11.10. Properties (the Other Half Of The Rdf Schema).
11.11. The Differences Between Classes And Properties.
11.12. Creating Instances Of Classes.
11.13. Preserving Namespaces For Classes And Properties.
11.14. Validating Rdf.
11.15. Rdf, Semantic Logic And Biomedical Ontologies.
11.16. Data Specifications Contrasted With Data Standards.
11.17. Specifying Data With Notation 3.
11.18. Rdf Reduces Complexity.
11.19. Perl Metadata Modules.
11.20. Chapter Summary.
12. Mathematical Functions.
12.1. Background.
12.2. Simple Addition.
12.3. Cumulative Addition Of A Column Of Numbers.
12.4. Posix.
12.5. A No-fuss Cosine Wave.
12.6. Perl Modules For Mathematics.
12.7. Using The Fast Fourier Transform Module.
13. Statistics and Epidemiology.
13.1. Background.
13.2. Simple Statistics.
13.3. Computing The Sample Standard Deviation From An Array Of Numbers.
13.4. Perl Modules For Statistics.
13.6. Seer Statistics.
13.7. Receiver Operator Characteristic (roc) Curves.
14. Modeling Biological and Medical Systems.
14.1. Background.
14.2. Using Random Numbers.
14.3. Resampling And Monte Carlo Statistics.
14.4. Rough Test Of The Built-in Random Number Generator.
14.5. How Often Can I Have A Bad Day?
14.6. The Monty Hall Problem: Solving What We Cannot Grasp.
15. Bioinformatics.
15.1. Background.
15.2. Perl Modules For Bioinformatics.
15.3. Bioperl Project.
15.4. Finding Palindromes In A Gene Database.
15.5. Clustering: Algorithms That Group Similar Objects.
16. Network Computing.
16.1. Background.
16.2. Perl Internet Modules.
16.3. Ftp.
16.4. Some Definitions.
16.5. Mailings.
16.6. Client-server On A Single Computer With Perl.
16.7. A Web Service Resource For Perl.
17. A Quick Peek at Object-Oriented Programming.
17.1. Background.
17.2. Overview Of Object-oriented Programming.
17.3. Object-oriented Programming In Perl.
18. Use-Case: A Digital Image Specification in RDF.
18.1. Background.
18.2. An Approach To Data Specification.
18.3. Creating An Rdf Schema For A Data Object.
18.4. Using The Rdf Schema To Specify Data Objects In Rdf.
18.5. Use-case: The Laboratory Digital Imaging Project.
18.6. The Rdf Schema Is Prepared From A Cde List.
18.7. Review Of Rdf Schema Properties.
18.8. The Jpeg Images.
18.9. Sample Textual Annotation.
18.10. Five Options For Preparing An Rdf Specification For An Image Object.
18.11. Option One: Rdf Document With Pointer To Image File.
18.12. Option Two: Rdf Document Containing Image Binary Converted To Base64 Ascii.
18.13. Converting A Jpg (binary) Image File To Base64.
18.14. Option Three: Inserting An Rdf Document Into A Jpeg Header.
18.15. Option Four: Specifying An Image With Multiple Rdf Files.
18.16. Option Five: Specifying Multiple Image Files And Multiple Rdf Documents.
18.17. Porting Between Data Specifications And Data Standards.
18.18. Chapter Summary.
19. Use-Case: Data Mining OMIM (Online Mendelian Inheritance in Man). 19.1. Background.
19.2. The Hypotheses.
19.3. The Specific Questions.
19.4. The Data.
19.5. Approach.
19.6. Functions Of The Perl Script.
19.7. Hashing Neoplasm Terms.
19.8. Assigning Lineage To Matched Neoplasms Terms.
19.9. Counting And Classifying The Omim Records Containing Neoplasm Terms.
19.10. Examining The Results.
19.11. Discussion.
19.12. A General Approach To Data Mining.
20. References (Commented).
21. Appendix.
21.1. Open Source Bioperl, Biopython, Bioruby.
21.2. Open Source Compression And Archiving Utilities (gzip, Gunzip, Tar, 7-zip, Bunzip).
21.3. R Open Source Statistical Programming Language And Bioconductor.
21.4. Cygwin, Open Source Unix/linux Emulator.
21.5. Gnupg, Open Source Encryption Tool.
21.6. Wget Web Site Mirroring Software.
21.7. Cwm, A Closed World Machine For Rdf (in Python).
21.8. Database Issue Of Nucleic Acids Research.
21.9. Umls Metathesaurus.
21.10. Mesh (the National Library Of Medicine's Medical Subject Headings).
21.11. Taxonomy.
21.12. Locuslink And Its Successor, Entrez Gene.
21.13. Sourceforge.
21.14. Cvs, Concurrent Versions System.
21.15. Cpan, The Comprehensive Perl Archive Network.
21.16. Omim - Online Mendelian Inheritance In Man.
21.17. Loinc, Logical Observations Identifiers, Names, And Codes.
21.18. Hl7 - Health Level 7.
21.19. Seer.
21.20. Umls Metathesaurus.
21.21. Medical Subject Headings - Mesh.
21.22. Gene Ontology - Go.
21.23. Obo (open Biology Ontologies).
21.24. Neoplasm Classification.
21.25. Us Census.
22. Glossary.
23. List of Perl Scripts.
24. Index.
25. Nota Bene.
26. Author Biography.

Library of Congress Subject Headings for this publication:

Perl (Computer program language).
Medicine -- Data processing.
Biology -- Data processing.