Data and Text Processing for Health and Life Sciences

by Francisco Couto

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Book Description

This book is a step-by-step introduction on how shell scripting can help solve many of the data processing tasks that Health and Life specialists face everyday with minimal software dependencies. The examples presented in the book show how simple command line tools can be used and combined to retrieve data and text from web resources, to filter and mine literature, and to explore the semantics encoded in biomedical ontologies. To store data this book relies on open standard text file formats, such as TSV, CSV, XML, and OWL, that can be open by any text editor or spreadsheet application.

The first two chapters, Introduction and Resources, provide a brief introduction to the shell scripting and describe popular data resources in Health and Life Sciences. The third chapter, Data Retrieval, starts by introducing a common data processing task that involves multiple data resources. Then, this chapter explains how to automate each step of that task by introducing the required commands line tools one by one. The fourth chapter, Text Processing, shows how to filter and analyze text by using simple string matching techniques and regular expressions. The last chapter, Semantic Processing, shows how XPath queries and shell scripting is able to process complex data, such as the graphs used to specify ontologies.

Besides being almost immutable for more than four decades and being available in most of our personal computers, shell scripting is relatively easy to learn by Health and Life specialists as a sequence of independent commands. Comprehending them is like conducting a new laboratory protocol by testing and understanding its procedural steps and variables, and combining their intermediate results. Thus, this book is particularly relevant to Health and Life specialists or students that want to easily learn how to process data and text, and which in return may facilitate and inspire them to acquire deeper bioinformatics skills in the future.

This open book is licensed under a Creative Commons License (CC BY). You can download Data and Text Processing for Health and Life Sciences ebook for free in PDF format (3.0 MB).

Table of Contents

Chapter 1
Introduction
 
Biomedical Data Repositories
 
Scientific Text
 
Amount of Text
 
Ambiguity and Contextualization
 
Biomedical Ontologies
 
Programming Skills
 
Why This Book?
 
How This Book Helps Health and Life Specialists?
 
What Is in the Book?
Chapter 2
Resources
 
Biomedical Text
 
Semantics
 
Further Reading
Chapter 3
Data Retrieval
 
Caffeine Example
 
Unix Shell
 
Web Identifiers
 
Data Retrieval
 
Data Extraction
 
Task Repetition
 
XML Processing
 
Text Retrieval
 
Further Reading
Chapter 4
Text Processing
 
Pattern Matching
 
Regular Expressions
 
Position
 
Tokenization
 
Entity Recognition
 
Pattern File
 
Relation Extraction
 
Further Reading
Chapter 5
Semantic Processing
 
Classes
 
URIs and Labels
 
Synonyms
 
Parent Classes
 
Ancestors
 
My Lexicon
 
Generic Lexicon
 
Performance
 
Entity Linking
 
Large Lexicons
 
Further Reading

Book Details

Subject
Medical
Publisher
Springer
Published
2019
Pages
107
Edition
1
Language
English
ISBN13
9783030138448
ISBN10
3030138445
ISBN13 Digital
9783030138455
ISBN10 Digital
3030138453
PDF Size
3.0 MB
License
CC BY

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