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Abstract

Ontology as a branch of philosophy is the science of what is, of the kinds and structures of objects, properties, events, processes and relations in every area of reality. The earliest use of the term 'ontology' (or 'ontologia') seems to have been in 1606 in the book Ogdoas Scholastica by the German Protestant scholastic Jacob Lorhard. For Lorhard, as for many subsequent philosophers, 'ontology' is a synonym of 'metaphysics' (a label meaning literally: 'what comes after the Physics'), a term used by early students of Aristotle to refer to what Aristotle himself called 'first philosophy'. Some philosophers use 'ontology' and 'metaphysics' to refer to two distinct, though interrelated, disciplines, the former to refer to the study of what might exist; the latter to the study of which of the various alternative possible ontologies is in fact true of reality. The term - and the philosophical discipline of ontology - has enjoyed a chequered history since 1606, with a significant expansion, and consolidation, in recent decades. We shall not discuss here the successive rises and falls in philosophical acceptance of the term, but rather focus on certain phases in the history of recent philosophy which are most relevant to the consideration of its recent advance, and increased acceptance, also outside the discipline of philosophy.

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Abstract

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.