Introduction to Bio-Ontologies

Introduction to Bio-Ontologies

by Peter N. Robinson, Sebastian Bauer

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Product Details

ISBN-13: 9781439836668
Publisher: CRC Press
Publication date: 06/22/2011
Series: Chapman & Hall/CRC Mathematical and Computational Biology
Sold by: Barnes & Noble
Format: NOOK Book
Pages: 517
File size: 3 MB

About the Author

Peter N. Robinson is a research scientist and leader of the Computational Biology Group in the Institute of Medical Genetics and Human Genetics at Charité-Universitätsmedizin Berlin. Dr. Robinson completed his medical education at the University of Pennsylvania, followed by an internship at Yale University. He also studied mathematics and computer science at Columbia University. His research interests involve the use of mathematical and bioinformatics models to understand biology and hereditary disease.

Sebastian Bauer is a research assistant in the Institute of Medical Genetics and Human Genetics at Charité-Universitätsmedizin Berlin. He earned a degree in computer science from the Technical University of Ilmenau. His research interests include mathematical modeling, discrete algorithms, theoretical computer science, software engineering, and the applications of these fields to medicine and biology.

Table of Contents

BASIC CONCEPTS
Ontologies and Applications of Ontologies in Biomedicine
What Is an Ontology?
Ontologies and Bio-Ontologies
Ontologies for Data Organization, Integration, and Searching
Computer Reasoning with Ontologies
Typical Applications of Bio-Ontologies

Mathematical Logic and Inference
Representation and Logic
Propositional Logic
First-Order Logic
Sets
Description Logic

Probability Theory and Statistics for Bio-Ontologies
Probability Theory
Bayes’ Theorem
Introduction to Graphs
Bayesian Networks

Ontology Languages
OBO
RDF and RDFS
OWL and the Semantic Web

BIO-ONTOLOGIES
The Gene Ontology
A Tool for the Unification of Biology
Three Subontologies
Relations in GO
GO Annotations
GO Slims

Upper-Level Ontologies
Basic Formal Ontology
The Big Divide: Continuants and Occurrents
Universals and Particulars
Relation Ontology
Revisiting Gene Ontology
Revisiting GO Annotations

A Selective Survey of Bio-Ontologies
OBO Foundry
The National Center for Biomedical Ontology
Bio-Ontologies
What Makes a Good Ontology?

GRAPH ALGORITHMS FOR BIO-ONTOLOGIES
Overrepresentation Analysis
Definitions
Term-for-Term
Multiple Testing Problem
Term-for-Term Analysis: An Extended Example
Inferred Annotations Lead to Statistical Dependencies in Ontology DAGs
Parent-Child Algorithms
Parent-Child Analysis: An Extended Example
Topology-Based Algorithms
Topology-elim: An Extended Example
Other Approaches
Summary

Model-Based Approaches to GO Analysis
A Probabilistic Generative Model for GO Enrichment Analysis
A Bayesian Network Model
MGSA: An Extended Example
Summary

Semantic Similarity
Information Content in Ontologies
Semantic Similarity of Genes and Other Items Annotated by Ontology Terms
Statistical Significance of Semantic Similarity Scores

Frequency-Aware Bayesian Network Searches in Attribute Ontologies
Modeling Queries
Probabilistic Inference for the Items
Parameter-Augmented Network
The Frequency-Aware Network
Benchmark

INFERENCE IN ONTOLOGIES
Inference in the Gene Ontology
Inference over GO Edges
Cross-Products and Logical Definitions

RDFS Semantics and Inference
Definitions
Interpretations
RDF Entailment
RDFS Entailment
Entailment Rules
Summary

Inference in OWL Ontologies
The Semantics of Equality
The Semantics of Properties
The Semantics of Classes
The Semantics of the Schema Vocabulary
Conclusions

Algorithmic Foundations of Computational Inference
The Tableau Algorithm
Developer Libraries

SPARQL
SPARQL Queries
Combining RDF Graphs
Conclusions

Appendix A: An Overview of R
Appendix B: Information Content and Entropy
Appendix C: W3C Standards: XML, URIs, and RDF
Appendix D: W3C Standards: OWL

Bibliography

Index

Exercises and Further Reading appear at the end of each chapter.

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