Basic Formal Ontology (BFO)

Related Material

Diagrams and Papers on Medical Ontology (MedO) and Geographic Ontology (GeO)

For experimental purposes the Medical Ontology (MedO) and the Geographic Ontology (GeO) have been created.

Diagrams

• MedO Diagram
• GeO Diagram

Papers

• Pierre Grenon, Barry Smith and Louis Goldberg: "Biodynamic Ontology: Applying BFO in the Biomedical Domain"
• Thomas Bittner and Barry Smith: "Normalizing Medical Ontologies using Basic Formal Ontology"
• Jonathan Simon and Barry Smith: "Using Philosophy to Improve the Coherence and Interoperability of Applications Ontologies"
• Thomas Bittner: "Formal Ontologies for Space and Time"

WonderWeb

• Claudio Masolo, Stefano Borgo, Aldo Gangemi, Nicola Guarino and Alessandro Oltramari: "WonderWeb Deliverable D18: Ontology Library"

Papers on Ontology and Formal Ontology

The Big Picture

• Barry Smith: "Logic and Formal Ontology"
• Barry Smith: "Basic Tools of Formal Ontology"
• Barry Smith: "Ontology"

On Concepts

• Barry Smith: "Beyond Concepts: Ontology as Reality Representation"
• Ingvar Johansson: "Bioinformatics and Biological Reality"

Ontology Terminology

• Barry Smith, Waclaw Kusnierczyk, Daniel Schober and Werner Ceusters: "Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain"

Papers on Best Ontology Practices

• Barry Smith, Jacob Köhler and Anand Kumar: "On the Application of Formal Principles to Life Science Data: A Case Study in the Gene Ontology"
• Werner Ceusters , Barry Smith, Louis Goldberg: "A Terminological and Ontological Analysis of the NCI Thesaurus"
• Jacob Köhler, Katherine Munn, Alexander Rüegg, Andre Skusa, Barry Smith: "Quality Control for Terms and Definitions in Ontologies and Taxonomies"
• Werner Ceusters and Barry Smith: "A Realism-Based Approach to the Evolution of Biomedical Ontologies"
• Barry Smith: "Against Idiosyncrasy in Ontology Development"

Papers on Specific Ontological Issues

Taxonomy and Classification

• Barry Smith: "The Logic of Biological Classification and the Foundations of Biomedical Ontology"
• Ingvar Johansson: "Four Kinds of 'Is_A' Relations"

Relations

• Thomas Bittner, Maureen Donnelly and Barry Smith: "Individuals, Universals and Collections: On the Foundational Relations of Ontology"
• Barry Smith and Cornelius Rosse: "The Role of Foundational Relations in the Alignment of Biomedical Ontologies"
• Barry Smith, Werner Ceusters, Bert Klagges, Jacob Köhler, Anand Kumar, Jane Lomax, Chris Mungall, Fabian Neuhaus, Alan L. Rector and Cornelius Rosse: "Relations in Biomedical Ontologies"
• Mathias Brochhausen: "The Derives_From Relation in Biomedical Ontologies"
• More about "Relations in Biomedical Ontologies"

Ontological Topics

• Ludwig Jansen: "Tendencies and other Realizables in Medical Information Sciences
• Barry Smith: "Mereotopology: A Theory of Parts and Boundaries"
• Fabian Neuhaus, Pierre Grenon, Barry Smith: "A Formal Theory of Substances, Qualities, and Universals"
• Barry Smith: "Boundaries: An Essay in Mereotopology"
• Ludger Jansen: "The Ontology of Tendencies and Medical Information Science"
• More about Fiat Objects
• More about Granular Partitions