Introduction to Bio-Ontologies

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Features

  • Describes a host of bio-ontologies, including Gene Ontology, Chemical Entities of Biological Interest, and Human Phenotype Ontology
  • Covers graph algorithms and inference algorithms
  • Explains how ontological algorithms are used in biological and biomedical applications
  • Offers overviews of the R programming language and the W3C standards of XML, RDF, and OWL
  • Supplies extensive references to the primary literature as well as pointers to important books and articles
  • Includes many theoretical and practical exercises
  • Provides software and data on a supporting website

Summary

Introduction to Bio-Ontologies explores the computational background of ontologies. Emphasizing computational and algorithmic issues surrounding bio-ontologies, this self-contained text helps readers understand ontological algorithms and their applications.

The first part of the book defines ontology and bio-ontologies. It also explains the importance of mathematical logic for understanding concepts of inference in bio-ontologies, discusses the probability and statistics topics necessary for understanding ontology algorithms, and describes ontology languages, including OBO (the preeminent language for bio-ontologies), RDF, RDFS, and OWL.

The second part covers significant bio-ontologies and their applications. The book presents the Gene Ontology; upper-level ontologies, such as the Basic Formal Ontology and the Relation Ontology; and current bio-ontologies, including several anatomy ontologies, Chemical Entities of Biological Interest, Sequence Ontology, Mammalian Phenotype Ontology, and Human Phenotype Ontology.

The third part of the text introduces the major graph-based algorithms for bio-ontologies. The authors discuss how these algorithms are used in overrepresentation analysis, model-based procedures, semantic similarity analysis, and Bayesian networks for molecular biology and biomedical applications.

With a focus on computational reasoning topics, the final part describes the ontology languages of the Semantic Web and their applications for inference. It covers the formal semantics of RDF and RDFS, OWL inference rules, a key inference algorithm, the SPARQL query language, and the state of the art for querying OWL ontologies.

Web Resource
Software and data designed to complement material in the text are available on the book’s website: http://bio-ontologies-book.org The site provides the R Robo package developed for the book, along with a compressed archive of data and ontology files used in some of the exercises. It also offers teaching/presentation slides and links to other relevant websites.

This book provides readers with the foundation to use ontologies as a starting point for new bioinformatics research projects or to support current molecular genetics research projects. By supplying a self-contained introduction to OBO ontologies and the Semantic Web, it bridges the gap between both fields and helps readers see what each can contribute to the analysis and understanding of biomedical data.

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.

Author Bio(s)

Editorial Reviews

"This book is one of the first source books in the field; it is well written and coherent. Its introduction gives the reader a good taste of what comes next and it also contains good exercises."
—Mohsen Mahmoudi Aznaveh, ACM SIGACT News, 2013

"This welcome book could have been titled ‘all you wanted to know about bio-ontologies but didn’t dare ask.’ In recent years the biological sciences have generated very large, complex data sets whose management, analysis and sharing have created unprecedented challenges. The development of ontologies, originally driven by the invention of the semantic web, has been critical in handling this data and permitting interoperability between databases and between applications. Many of the bio-ontologies and the computational approaches which use them have now become mature, and an understanding of bio-ontologies has really become a requirement for anyone in the mainstream biomedical sciences.
Introduction to Bio-Ontologies provides a self-contained introduction to ontologies for bioinformaticians, computer scientists and biomedical scientists who need to know about the computational background and implementation of ontologies. The book is designed to support either advanced undergraduate or master’s courses in bioinformatics or computer science but is also a first stop for any investigator who wants to understand ontologies and how to use them.
The four parts of the book cover basic concepts, specific widely used ontologies, such as the Gene Ontology, algorithms and applications of ontologies. The breadth of coverage is impressive for such a compact volume and there is excellent critical discussion of ontologies from a biological as well as a computational point of view. The book succeeds well in its aim of providing a self-contained primer on ontologies and much of the mathematics used is backed up with detailed explanations and technical appendices which introduce and explain the more complex mathematical and logical concepts, such as inference and information content. Practical exercises are provided and these are very valuable for using the book as a teaching tool.
Well written, up to date and accessible this is an excellent addition to the bookshelves of any lab and could be the core text for a course on ontologies."
—Dr. Paul Schofield, Senior Lecturer in Anatomy, Department of Physiology, Development and Neuroscience, University of Cambridge, UK

"This excellent book provides a clear and objective introduction to the subject, and provides an extensive and detailed overview of state-of-the-art research towards a more efficient exploitation of the existing and newly generated biomedical data by using bio-ontologies. As a professor I intend to adopt this book for graduate course-units on bioinformatics and as a researcher I intend to use this book as a way to introduce me to state-of-the-art approaches related to my research interests."
—Francisco M. Couto, University of Lisbon, Portugal