Introduction to Bio-Ontologies

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