Publications
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
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
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
Dissertations
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"
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
- Katherine Munn, Barry Smith (Eds.): "Applied Ontology: An Introduction"
- Barry Smith (Ed.) "Parts and Moments: Studies in Logic and Formal Ontology"
- 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"
- Luc Schneider: "Revisiting the Ontological Square"
- Lars Vogt: "Spatio-structural granularity of biological material entities"
- Johannes öhl and Ludger Jansen: "Representing Dispositions"
- Barry Smith: "On Substances, Accidents and Universals: In Defence of a Constituent Ontology", Philosophical Papers, 26 (1997), 105-127
- Pierre Grenon and Barry Smith: "SNAP and SPAN: Towards Dynamic Spatial Ontology", Spatial Cognition and Computation, 4: 1 (March 2004), 69-103
- Barry Smith and Pierre Grenon: "The Cornucopia of Formal-Ontological Relations", Dialectica 58: 3 (2004), 279-296
- Barry Smith, Werner Ceusters, Bert Klagges, Jacob öhler, Anand Kumar, Jane Lomax, Chris Mungall, Fabian Neuhaus, Alan Rector and Cornelius Rosse: "Relations in Biomedical Ontologies", Genome Biology (2005), 6 (5), R46
- Thomas Bittner, Maureen Donnelly and Barry Smith: "A Spatio-Temporal Ontology for Geographic Information Integration", International Journal for Geographical Information Science, 23 (6), 2009, 765-798
- Barry Smith and Werner Ceusters: "Ontological Realism as a Methodology for Coordinated Evolution of Scientific Ontologies", Applied Ontology, 5 (2010), 139-188
- Barry Smith: "The Basic Tools of Formal Ontology", in Nicola Guarino (ed.), Formal Ontology in Information Systems Amsterdam, Oxford, Tokyo, Washington, DC: IOS Press (Frontiers in Artificial Intelligence and Applications), 1998, 19-28
- Barry Smith: "Against Fantology", in Johann C. Marek and Maria E. Reicher (eds.), Experience and Analysis, Vienna: HPT&ÖBV, 2005, 153-170
- Robert Arp and Barry Smith: "Function, Role, and Disposition in Basic Formal Ontology", Proceedings of Bio-Ontologies Workshop (ISMB 2008), Toronto, 45-48
- Lars Vogt, Peter Grobe, Björn Quast and Thomas Bartolomaeus: "Top-Level Categories of Constitutively Organized Material Entities - Suggestions for a Formal Top-Level Ontology"
- More about Fiat Objects
- More about Granular Partitions
Miscellaneous
- Viviana Mascardi, Valentina Cordi and Paolo Rosso: "A Comparison of Upper Ontologies"
- Maria Keet: "Examples: DOLCE and BFO in DL and Manchester syntax"
- David Salmen, Tatiana Malyuta, Alan Hansen, Shaun Cronen and Barry Smith: "Integration of Intelligence Data through Semantic Enhancement" (see project)
