What is An Ontology?

The word ‘ontology’ can refer to a branch of Western philosophy—having its origins in ancient Greece with philosophers such as Parmenides, Heraclitus, Plato, and Aristotle—the concern of which is the study of what is, of the kinds and structures of objects, properties, events, processes, and relations in every area of reality. From this philosophical perspective, ontology seeks to provide a definitive and exhaustive classification of entities in all spheres or domains of being. As a theoretical discipline concerned with accurately describing the taxonomy of all things that exist, philosophical ontology is synonymous with classical metaphysics.

This philosophical sense of the term is what Rudolf Göckel (1547-1628) and Jacob Lorhard (1561-1609) had in mind when they independently coined the term ‘ontology’ (ontologia). Ontology derives from the Greek words ontos (meaning “existence” or “being”) and logos(meaning “rational account” or “knowledge”), so it makes sense that Nathan Bailey’s 1721 Oxford English Dictionary defined ontology as “an Account of being in the Abstract” while, today, the Random House College Dictionary (2007) defines ontology as “the branch of metaphysics that studies the nature of existence.”

In fact, people are naturally philosophical ontologists of one sort or another since all of us form systems of classification as we try to understand, navigate, predict, and control the complex workings of this universe. For example, we sort things into genus/species or supertype/subtype hierarchical relationships of greater and lesser degrees of complexity. Consider, too, all of the models, illustrations, flow charts, schematizations, and other pictorial renditions—like Linnean Cladistics in biology and the Periodic Table of the Elements in chemistry—that utilize a philosophically ontological categorization in order to capture the classification of entities and their relationships to one another. In many ways, the contemporary classification techniques we utilize today in several areas of study and practice have their genesis in Aristotle’s (ca. 384-322 BCE) common-sense ideas, arguments, and methodologies.

Related to this philosophical sense, since the emergence of the information age ‘ontology’ also has come to be understood as a structured, taxonomic model or representation of the entities and relations existing within a particular domain of reality. There exists the Gene Ontology, Infectious Disease Ontology, Friend of a Friend, and numerous others. Domain ontologies, thus, are contrasted with ontology in the philosophical sense, which has all of reality as its subject matter.

Start with the Wikipedia page dealing with ontologies, but also look at the W3C Semantic Web, Web Ontology Language (OWL) materials, along with papers by Tom Gruber, Peter F. Patel-Schneider, Ian Horrocks, Jim Hendler, Pat Hayes, and Deborah McGuinness.

Further, see the chapter titled, “The Interplay between Ontology as Categorical Analysis and Ontology as Technology” by Roberto Poli and Leo Obrst in Theory and Applications of Ontology: Computer Applications (Springer, 2010).

Also, a standard introductory text for the working ontologist is Dean Allemang and Jim Hendler’s Semantic Web for the Working Ontologist.

Barry Smith, Andrew Spear, and I finished up a book we published through MIT Press called Building Ontologies with Basic Formal Ontology. (These two scholars are inspirations to me.) For years now, many researchers from all over the world have requested such a book, especially members of the Open Biological and Biomedical Ontologies Foundry. Our book will refer to the Ontology for General Medical Science, which is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, such as disease, disorder, diagnosis, patient, healthcare provider, and others. OGMS uses Basic Formal Ontology as an upper-level ontology.

Click here for an early draft of one of the chapters of the book where we lay out the history of the development of the Web Ontology Language (OWL).

Click here for a basic, layperson’s explanation of an ontology in a paper I produced for a magazine calledUndersea Warfare, the official publication of the U.S. Submarine Force.

A Few of My Articles

Besides my book, Building Ontologies with Basic Formal Ontology (MIT Press, 2015) with Barry Smith and Andrew Spear, I have published the following articles:

  • “A New Role for Ontology in the History of Western Philosophy,” Philosophia, revise and re-submit.
  • “An Introduction to Information Ontologies,” Techné: Research in Philosophy and Technology, revise and re-submit.
  • “Ontology: Not Just for Philosopher’s Anymore,” Practical Philosophy, (2010) 10: 81-103.
  • “Radiological and Biomedical Knowledge Integration: The Ontological Way,” with Rethy Chhem, Cesare Romagnoli, and James Overton, in Scholarship in Radiology Education: The Scholarship of Teaching and Learning (chapter 8, pp. 87-104). Rethy Chhem, Kathy Hilbert, and Teresa Van Deven (eds.), Springer, 2009.
  • “Function, Role, and Disposition in Basic Formal Ontology,” with Barry Smith, Nature Precedings, (2008) 1941, 1.
  • “Realism and Antirealism in Informatics Ontologies,” The American Philosophical Association: Philosophy and Computers (2009) 9, 1: 19-23.
  • “Creating a Controlled Vocabulary for the Ethics of Human Research: Towards a Biomedical Ethics Ontology,” with David Koepsell, Jennifer Fostel, and Barry Smith. The Journal of Empirical Research on Human Research Ethics (2009) 4: 43-58.
  • “Ontologies Just May Save Your Savings Accounts,” in Progress in Economics Research, Volume 16. (chapter 6, pp. 115-129). Albert Tavidze (ed.), Nova Publishers, 2010.
  • “Ontologies of Cellular Networks,” with Barry Smith, Science Signaling (2008) 1: mr2.
  • “Philosophical Ontology,” “Domain Ontology,” and “Formal Ontology,” in Key Terms in Logic, Jon Williamson and Federica Russo (eds.). Bloomsbury Press, 2010: 74-75.
  • “Philosophical, Domain, and Formal Ontology.” The Reasoner (2008) 1: 12.
  • “The Referent Tracking System as a Peer 2 Peer Application,” with Shahid Manzoor, Werner Ceusters, and Ron Rudnicki, Proceedings of the 9th IASTED International Conference Software Engineering and Applications (SEA 2008) 112-117.