ABSTRACT
The word ontology has been in use for many years, and was originally used to describe a branch of metaphysics concerned with the nature and relations of being. More recently, the word ontology has been used to refer to a common, controlled knowledge representation designed to help knowledge sharing and computer reasoning. In this book, we will cover certain kinds of ontologies in common use in biomedical research called bio-ontologies, which have become an essential feature of many fields of biomedical research in which large amounts of data are handled. Bio-ontologies represent a challenging and rewarding field in computational biology and bioinformatics, because practitioners need to know not only about a wide range of algorithms and computational algorithms and to integrate multiple kinds of data from multiple sources, but must also understand the logical and philosophical underpinnings of ontologies to perform computer reasoning and to express and analyze the meaning of the data under study. To build an ontology is an intellectually stimulating exercise that amounts to constructing a philosophical and computational model of the world, or at least of some small part of it.
