Data and Text Processing for Health and Life Sciences
Springer, 2019 - 98 páginas
This open access 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.
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acronyms Alport syndrome alternative Andersen-Tawil syndrome argument caffeine chapter character ChEBI chebi_lite.owl command line tool Couto Creative Commons licence curl data and text database dbReference type="PubMed Disease Ontology diseases.txt chebi_27732_sentences.txt DiShIn doid echo http://purl.obolibrary element entities entry equivalent long form European Bioinformatics Institute Exact Synonym example execute the script extract following command format gawk F getlabels.sh doid.owl getparents.sh getproteins.sh geturi.sh doid.owl grep command http://purl http://purl.obolibrary.org/obo labels lexicon list of proteins local-name LQT1 malignant hyperthermia mention MH[SNE MISCELLANEOUS multiple myfile.txt numerical digit obolibrary.org/obo obolnOwl option output OWL file parents pattern PubMed purl.obolibrary.org/obo rdf:datatype="http redirection operator regular expressions related to caffeine represents retrieve reversemyfile.sh ryanodine receptor Semantic similarity sentences shell scripting sort specific standard input string terminal application text editor text processing UniProt Unix shell xargs xmllint xpath XPath query