Data and Text Processing for Health and Life Sciences.

• Superior document: Advances in Experimental Medicine and Biology Series ; v.1137
• Author: Couto, Francisco M.
• Place / Publishing House: Cham : : Springer International Publishing AG,, 2019.; Ã2019.
• Year of Publication: 2019
• Edition: 1st ed.
• Language: English
• Series: Advances in Experimental Medicine and Biology Series
• Physical Description: 1 online resource (107 pages)

Table of Contents

Intro -- Preface -- Acknowledgments -- Contents -- Acronyms -- 1 Introduction -- Biomedical Data Repositories -- Scientific Text -- Amount of Text -- Ambiguity and Contextualization -- Biomedical Ontologies -- Programming Skills -- Why This Book? -- Third-Party Solutions -- Simple Pipelines -- How This Book Helps Health and Life Specialists? -- Shell Scripting -- Text Files -- Relational Databases -- What Is in the Book? -- Command Line Tools -- Pipelines -- Regular Expressions -- Semantics -- 2 Resources -- Biomedical Text -- What? -- Where? -- How? -- Semantics -- What? -- Languages -- Formality -- Gold Related Documents -- Where? -- OBO Ontologies -- Popular Controlled Vocabularies -- How? -- OWL -- URI -- Further Reading -- 3 Data Retrieval -- Caffeine Example -- Unix Shell -- Current Directory -- Windows Directories -- Change Directory -- Useful Key Combinations -- Shell Version -- Data File -- File Contents -- Reverse File Contents -- My First Script -- Line Breaks -- Redirection Operator -- Installing Tools -- Permissions -- Debug -- Save Output -- Web Identifiers -- Single and Double Quotes -- Comments -- Data Retrieval -- Standard Error Output -- Data Extraction -- Single and Multiple Patterns -- Data Elements Selection -- Task Repetition -- Assembly Line -- File Header -- Variable -- XML Processing -- Human Proteins -- PubMed Identifiers -- PubMed Identifiers Extraction -- Duplicate Removal -- Complex Elements -- XPath -- Namespace Problems -- Only Local Names -- Queries -- Extracting XPath Results -- Text Retrieval -- Publication URL -- Title and Abstract -- Disease Recognition -- Further Reading -- 4 Text Processing -- Pattern Matching -- Case Insensitive Matching -- Number of Matches -- Invert Match -- File Differences -- Evaluation Metrics -- Word Matching -- Regular Expressions -- Extended Syntax -- Alternation -- Basic Syntax.

Scope -- Multiple Alternatives -- Multiple Characters -- Spaces -- Groups -- Ranges -- Negation -- Quantifiers -- Optional -- Multiple and Optional -- Multiple and Compulsory -- All Options -- Position -- Beginning -- Ending -- Near the End -- Word in Between -- Full Line -- Match Position -- Tokenization -- Character Delimiters -- Wrong Tokens -- String Replacement -- Multi-character Delimiters -- Keep Delimiters -- Sentences File -- Entity Recognition -- Select the Sentence -- Pattern File -- Relation Extraction -- Multiple Filters -- Relation Type -- Remove Relation Types -- Further Reading -- 5 Semantic Processing -- Classes -- OWL Files -- Class Label -- Class Definition -- Related Classes -- URIs and Labels -- URI of a Label -- Label of a URI -- Synonyms -- URI of Synonyms -- Parent Classes -- Labels of Parents -- Related Classes -- Labels of Related Classes -- Ancestors -- Grandparents -- Root Class -- Recursion -- Iteration -- My Lexicon -- Ancestors Labels -- Merging Labels -- Ancestors Matched -- Generic Lexicon -- All Labels -- Problematic Entries -- Special Characters Frequency -- Completeness -- Removing Special Characters -- Removing Extra Terms -- Removing Extra Spaces -- Disease Recognition -- Performance -- Inverted Recognition -- Case Insensitive -- ASCII Encoding -- Correct Matches -- Incorrect Matches -- Entity Linking -- Modified Labels -- Ambiguity -- Surrounding Entities -- Semantic Similarity -- Measures -- DiShIn Installation -- Database File -- DiShIn Execution -- Large Lexicons -- MER Installation -- Lexicon Files -- MER Execution -- Further Reading -- Bibliography -- Index.