Data and Text Processing for Health and Life Sciences.
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| Superior document: | Advances in Experimental Medicine and Biology Series ; v.1137 |
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| 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
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| Online Access: | |
| Physical Description: | 1 online resource (107 pages) |
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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.