Robert Arp, Barry Smith, and Andrew Spear
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
Ontologies Are 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
Universals and Particulars
Empty or Potentially Empty General Terms
Universal vs. Class
Relations in Ontologies
Further Reading on Issues of Epistemological and Ontological Realism
Philosophical Ontology and Taxonomy
Formal vs. Material Ontologies
Domain Ontology and Taxonomy
Definition, Taxonomy, Ontology
Choice of Top-Level Ontology
Application vs. Reference Ontology
Further Reading on Top-Level and Domain Ontology
Further Reading on Taxonomy and Classification
General Principles of Ontology Design
Additional Principles of Ontology Design
5. The Principle of Reuse
6. The Ontology Design Process Should Balance Utility and Realism
7. The Ontology Design Process Is Open-Ended
8. 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
The Problem of Nonexistents
Further Reading on Relevance, Perspectivalism, Granularity, and Adequatism
Principles for Terminology
Gather and Select Terminology
1. Include in the terminology terms used by scientists
2. Strive to ensure maximal consensus with the scientists’ usage
3. Identify areas of disciplinary overlap where terminological usage is not consistent
4. In terminology construction and ontology design, make use of as many existing resources (terminologies and ontologies) as possible.
5. Use singular nouns.
6. Use lowercase for common nouns.
7. Avoid acronyms.
8. Associate each term in the ontology with a unique alphanumeric identifier.
9. Ensure univocity of terms.
10. Ensure univocity of relational expressions.
11. Avoid mass terms.
12. Distinguish the general from the particular.
Principles for Definitions
13. Provide all nonroot terms with definitions
14. Use Aristotelian definitions
15. Use essential features in defining terms.
16. Start with the most general terms in your domain.
17. Avoid circularity in defining terms.
18. To ensure the intelligibility of definitions, use simpler terms than the term you are defining.
19. Do not create terms for universals through logical combination.
20. Definitions should be unpackable (Term-definition intersubstitutability)
Principles for Taxonomies
21. Structure every ontology around a backbone is_a hierarchy.
22. Ensure is_a completeness.
23. Ensure asserted single inheritance.
24. Both developers and users of an ontology should respect the open-world assumption.
25. Adhere to the rule of objectivity, which means: describe what exists in reality, not what is known about what exists in reality
Further Readings on Definitions and Categorization
Examples of Critical Reviews
Some Basic Features of BFO
Basic Types of Entity: Continuant and Occurrent
BFO: Independent Continuant
BFO: Material Entity
BFO: Object Aggregate
BFO: Fiat Object Part
BFO: Specifically Dependent Continuant
BFO: Relational Quality
Relations That Do and Relations That Do Not Have Instances
BFO: Realizable Entity
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: 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
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 in Practice
Further Reading on Processes and Events
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
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
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