Building Ontologies with Basic Formal Ontology

by Robert Arp, Barry Smith, Andrew D. Spear

In the era of "big data," science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use.

After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies.

Genres: Philosophy, Computer Science, Computers

220 pages, Paperback

First published August 21, 2015

About the author

Robert Arp, Ph.D. (Saint Louis University, 2005), has taught Philosophy at Southwest Minnesota State University, Florida State University, and many schools in Missouri, before doing postdoctoral research in ontology through the National Center for Biomedical Ontology with Mark Musen and Barry Smith at the University at Buffalo.

Reviews

[Gregory · Rating 3 out of 5]

I picked up this book in part because the authors are philosophers by training, and I thought it would provide an interesting perspective on ontologies, which are an important tool in health information systems and bioinformatics. In fact, it does provide useful perspective, but I still found it disappointing.

The first part of the book provides background in philosophy, and offers a defense of realism (as opposed to nominalism and idealism). This is fine, and the authors provide some good arguments, but it isn't entirely clear (to me, at least) how this constitutes an argument for Basic a Formal Ontology (BFO), the formal framework, the exposition of which forms the main part of the book. There are hints, of course. For example, one of the authors' criticisms of OWL is that it allows for different classes to have the same set of elements (extension). Of course, this is hardly surprising for any system built on first order predicate logic!

The final section compares BFO with the main technologies used to enable the semantic web: Resource Description Format (RDF) and Web Ontology Language (OWL). The authors conclude that these technologies are either too weak or awkward to use, and they have a valid point but instead of discussing alternatives in any detail, they refer to an ontology editor known as Protégé. Indeed, extensive references are a strong point of the book. Overall, I'd like to see more focus on technology, and perhaps more discussion of the implications of the choice of mathematical foundations for a theory of ontologies. Then again, perhaps this outside the scope of the present book.

[Per Kraulis · Rating 4 out of 5]

As good an exposition of formal ontology has one could possibly get. Clear, methodical, and explicit about the philosophical underpinnings. It lacks a critique of the computational aspects. In my opinion, ontologies are not sufficiently integrated with the web. They are usually available as file dumps for loading into stand-alone software tools, while it seems obvious to me that an ontology should be first and foremost defined as a web service.

[Michiel · Rating 3 out of 5]

Good introduction to the topic. Would have liked it to be a bit more applied.

[Bruce]

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