Skip to main content

Building Ontologies with Basic Formal Ontology

by Robert Arp (Author), Barry Smith (Author), Andrew D. Spear (Author)

Building Ontologies with Basic Formal Ontology

About the book​

An introduction to the field of applied ontology with examples derived particularly from biomedicine, covering theoretical components, design practices, and practical applications. 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.

Detailed Table of Contents​

Introduction​

  • Overwhelmed with Information
  • Obstacles to Accessibility: Human and Technical Idiosyncrasy
  • The Computer Limitations Problem
  • Some Implications of Computer Limitations for Information Representation and Management
  • The Problem of Imprecise Thinking
  • An Example: The BRIDG Model
  • Ontology as Part of the Solution
  • A New Organon for the Information Age
  • Suggested Further Reading

1 What Is an Ontology?​

  • Introduction
  • Ontologies Are Representational Artifacts
  • Artifacts
  • Representational Artifacts
  • Representational Units and Composite Representations
  • A Note on "Term"
  • Ontology, Terminology, Conceptology
  • Ontology and Terminology: The Case of ISO
  • The Concept Orientation
  • Philosophical and Historical Background to Conceptualism
  • Realism and Ontology
  • Accurately Representing Entities in Reality
  • Respecting the Use-Mention Distinction
  • Ontologies Represent Universals, Defined Classes, and the Relations Between Them
  • The Goal of Science Is to Represent General Features of Reality
  • Ontological Realism
  • Metaphysical Nominalism
  • Universals and Particulars
  • Empty or Potentially Empty General Terms
  • Universal vs. Class
  • Relations in Ontologies
  • Basic Relations
  • Universal-Universal Relations
  • Universal-Particular Relations
  • Particular-Particular Relations
  • Conclusion
  • Further Reading on Issues of Epistemological and Ontological Realism

2 Kinds of Ontologies and the Role of Taxonomies​

  • Philosophical Ontology
  • Philosophical Ontology and Taxonomy
  • Simple Taxonomies
  • Formal vs. Material Ontologies
  • Domain Ontology
  • Domain Ontology and Taxonomy
  • Definition, Taxonomy, Ontology
  • Top-Level Ontology
  • Semantic Interoperability
  • Choice of Top-Level Ontology
  • Application vs. Reference Ontology
  • Conclusion
  • Further Reading on Top-Level and Domain Ontology
  • Further Reading on Taxonomy and Classification

3 Principles of Best Practice I: Domain Ontology Design​

  • General Principles of Ontology Design
      1. Realism
      1. Perspectivalism
      1. Fallibilism
      1. Adequatism
  • Additional Principles of Ontology Design
    • 5. The Principle of Reuse
      1. The Ontology Design Process Should Balance Utility and Realism
      1. The Ontology Design Process Is Open-Ended
      1. The Principle of Low-Hanging Fruit
  • Overview of the Domain Ontology Design Process
  • Explicitly Determine the Subject Matter of the Domain Ontology
  • Domain and Top-Level Ontologies
  • Relevance
  • Granularity
  • The Problem of Nonexistents
  • Conclusion
  • Further Reading on Relevance, Perspectivalism, Granularity, and Adequatism

4 Principles of Best Practice II: Terms, Definitions, and Classification​

  • Principles for Terminology
  • Gather and Select Terminology
      1. Include in the terminology terms used by scientists
      1. Strive to ensure maximal consensus with the scientists' usage
      1. Identify areas of disciplinary overlap where terminological usage is not consistent
      1. In terminology construction and ontology design, make use of as many existing resources as possible
  • Formatting Terminology
    • 5. Use singular nouns
      1. Use lowercase for common nouns
      1. Avoid acronyms
      1. Associate each term in the ontology with a unique alphanumeric identifier
      1. Ensure univocity of terms
      1. Ensure univocity of relational expressions
      1. Avoid mass terms
      1. Distinguish the general from the particular
  • Principles for Definitions
    • 13. Provide all nonroot terms with definitions
      1. Use Aristotelian definitions
      1. Use essential features in defining terms
      1. Start with the most general terms in your domain
      1. Avoid circularity in defining terms
      1. To ensure the intelligibility of definitions, use simpler terms than the term you are defining
      1. Do not create terms for universals through logical combination
      1. Definitions should be unpackable (Term-definition intersubstitutability)
  • Principles for Taxonomies
    • 21. Structure every ontology around a backbone is_a hierarchy
      1. Ensure is_a completeness
      1. Ensure asserted single inheritance
      1. Both developers and users of an ontology should respect the open-world assumption
      1. Adhere to the rule of objectivity: describe what exists in reality, not what is known about what exists
  • Conclusion
  • Further Readings on Definitions and Categorization
  • Examples of Critical Reviews

5 Introduction to Basic Formal Ontology I: Continuants​

  • Some Basic Features of BFO
  • Basic Types of Entity: Continuant and Occurrent
  • BFO: Continuant
  • BFO: Independent Continuant
  • BFO: Material Entity
  • BFO: Object
  • BFO: Object Aggregate
  • BFO: Fiat Object Part
  • Combination Object-Entities
  • BFO: Specifically Dependent Continuant
  • BFO: Quality
  • BFO: Relational Quality
  • Relations That Do and Relations That Do Not Have Instances
  • BFO: Realizable Entity
  • BFO: Role
  • BFO: Disposition
  • BFO: Function
  • BFO: Specifically Dependent Continuant: Summary
  • Reciprocal Dependence among Realizable Dependent Continuants
  • BFO: Generically Dependent Continuant
  • BFO: Immaterial Entity
  • BFO: Continuant Fiat Boundary (including Zero-, One-, and Two-Dimensional Continuant Fiat Boundary)
  • Boundaries and Granularity
  • BFO: Site
  • BFO: Spatial Region (including Zero-, One-, Two-, and Three-Dimensional Spatial Regions)
  • Spatial Regions and Frames of Reference
  • A BFO Continuant Classification
  • Further Reading on Basic Formal Ontology
  • Further Reading on Granularity
  • Further Reading on Independent Continuants
  • Further Reading on Dependent Continuants
  • Further Reading on Boundaries, Spatial Regions, and Topology

6 Introduction to Basic Formal Ontology II: Occurrents​

  • BFO: Process
  • BFO: History
  • BFO: Process Boundary
  • BFO: Spatiotemporal Region
  • BFO: Temporal Region
  • BFO: Zero-Dimensional Temporal Region
  • BFO: One-Dimensional Temporal Region
  • An Example of Occurrent Classification
  • Classifying Universals with BFO
  • Exhaustiveness of BFO Categories
  • BFO's Perspectivalism
  • BFO's Perspectivalism in Practice
  • Further Reading on Processes and Events

7 The Ontology of Relations​

  • BFO Relations
  • Relations: Formal Properties and Conventions
  • Primitive Instance-level Relations
  • Universal-Universal Relations in BFO
  • Foundational Relation: is_a
  • Foundational Relations: continuant_part_of and occurrent_part_of
  • Spatial and Temporal Relations
  • Spatial Relation: adjacent_to
  • Temporal Relation: derives_from
  • Temporal Relation: preceded_by
  • Participation Relation: has_participant
  • Some Further Top-Level Relations
  • proper_continuant_part_of and proper_occurrent_part_of
  • has_continuant_part and integral_continuant_part; has_occurrent_part and integral_occurrent_part
  • Relations and Definitions of Categories
  • The All-Some Rule
  • Inversion and Reciprocity
  • Some Examples of Axioms
  • Reflexivity, Symmetry, and Transitivity
  • Further Reading on Relations

8 Basic Formal Ontology at Work​

  • The Protégé Ontology Editor and BFO
  • The Web Ontology Language (OWL)
  • Hypertext Markup Language (HTML) and Extensible Markup Language (XML)
  • Resource Description Framework (RDF)
  • RDF Schema (RDFS)
  • Simple Protocol and RDF Query Language (SPARQL)
  • Basic Features of OWL
  • OWL vs. Standard Relational Databases
  • OWL 2
  • Building Ontologies with Basic Formal Ontology
  • Example: The Ontology for General Medical Science (OGMS)
  • Infectious Disease Ontology (IDO)
  • Information Artifact Ontology (IAO)
  • The Emotion Ontology (MFO-EM)
  • Facilitation of Interoperability
  • Further Reading in OWL, RDFS, and RDF

Appendices and References​

  • Appendix on Implementation: Languages, Editors, Reasoners, Browsers, Tools for Reuse
  • Glossary
  • Web Links Mentioned in the Text
  • Notes
  • Bibliography

Get the Book​

You can purchase this book from MIT Press or Amazon.

For more information about BFO, visit the BFO website.