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Ontology is the philosophical discipline which aims to understand how things in the world are divided into categories and how these categories are related together. This is exactly what information scientists aim for in creating structured, automated representations, called ‘ontologies,’ for managing information in fields such as science, government, industry, and healthcare. Currently, these systems are designed in a variety of different ways, so they cannot share data with one another. They are often idiosyncratically structured, accessible only to those who created them, and unable to serve as inputs for automated reasoning. This volume shows, in a non-technical way and using examples from medicine and biology, how the rigorous application of theories and insights from philosophical ontology can improve the ontologies upon which information management depends.

About the editors

Katherine Munn is a former researcher for the Institute for Formal Ontology and Medical Information Science and is currently reading for a PhD in philosophy at Oxford University.

Barry Smith is a prominent contributor to both theoretical and applied research in ontology. He is the author of some 450 scientific publications on ontology and related topics. Currently, the primary focus of his research is the application of ontology in biomedicine and biomedical informatics.

Table of Contents

Introduction: What is Ontology for?

Katherine Munn

Acknowledgments

1. Bioinformatics and Philosophy

Barry Smith and Bert Klagges

2. What Is Formal Ontology?

Boris Hennig

3. A Primer on Knowledge Management and Ontological Engineering

Pierre Grenon

4. New Desiderata for Biomedical Terminologies

Barry Smith

5. The Benefits of Realism: A Realist Logic with Applications

Barry Smith

6. A Theory of Granular Partitions

Thomas Bittner and Barry Smith

7. Classifications

Ludger Jansen

8. Categories: The Top-Level Ontology

Ludger Jansen

9. The Classification of Living Beings

Peter Heuer and Boris Hennig

10. Ontological Relations

Ulf Schwarz and Barry Smith

11. Four Kinds of ‘Is_A’ Relation

Ingvar Johansson

12. Occurrents

Boris Hennig

13. Bioinformatics and Biological Reality

Ingvar Johansson

References

Index