1. http://ontologist.com Upper Ontology Summit Tuesday March 14 The BFO perspective Barry Smith Department of Philosophy, University at Buffalo National Center for Ontological Research National Center for Biomedical Ontology

2. http://ontologist.com Basic Formal Ontology Basic Formal Ontology is a highest-common denominator upper ontology designed to support interoperability between domain ontologies developed to support shared use of scientific research data across disciplinary boundaries

3. http://ontologist.com Virtues of semantic interoperability for scientific and clinical research allows data to be reused across disciplinary boundaries allows communities to communicate across disciplinary boundaries allows communities to reuse the same software for managing their data

4. http://ontologist.com What is semantic? Model-theoretic (set-theoretic) semantics provided on the basis of full formalization? The meanings of terms are taken into account, rather than just syntax? The referents of terms are taken into account = what terms refer to in reality, rather than in some set-theoretic model?

5. http://ontologist.com The State of the Art (in Biomedical Ontology) Many domain ontologies are pre-formal artifacts Gene Ontology: hemolysis =def. the causes of hemolysis menopause part_of death Such ontologies can be conveyed in a variety of different formats; but much of their information content is not formal in nature, or is not yet formalized. Upper ontologies can help bring advances where one needs to work with pluralities of very large domain ontologies, some with several million terms

6. http://ontologist.com Virtues of upper ontologies for scientific and clinical research Early adoption of a high quality shared upper ontology by different communities can mean data is organized in compatible (semantically interoperable) ways Formal definitions, axiomatization and formal semantics of upper ontologies can add reasoning power to be used both within and between domain ontologies Can import formal rigor into domain ontologies (from the top)

7. http://ontologist.com Upper ontologies require domain ontologies with a need to intercommunicate Upper ontologies without domain ontologies are inherently partial artifacts (like telephone switchboards without subscribers)

8. http://ontologist.com Upper ontologies require users We agree that axioms and formal definitions are an indispensable part of creating semantic interoperability catalyzed through an upper ontology But an upper ontology will only be used by domain scientists if we provide humanly intelligible equivalents to these axioms and formal definitions These equivalent natural language axioms and definitions should conform to the intuitions of domain scientists Upper ontology is something like the common sense of domain scientists

9. http://ontologist.com The methodology of annotations Scientists perform experiments (including clinical trials) yielding huge amounts of data These experiments provide information about given types of entities in reality, e.g. that genes and proteins of this type are associated with this type of clinical phenomena Annotators create corresponding associations between gene and protein names in databases and terms from different domain ontologies such as the Gene Ontology Upper ontologies should help reasoning with this annotation information

10. http://ontologist.com Can we help? Need for a registry of upper ontologies National Center for Biomedical Ontology (http://ncbo.us) Bioportal = a registry of ontologies in the biomedical domain, including different sorts of metadata, supported by visualization and ontology integration tools

11. http://ontologist.com Can we help? A registry of upper ontologies should contain evaluation information, including information regarding actual usage. (Cf. NCOR Evaluation Project) There is a very small sub-lattice of concretely expressed theories being used in actual integration efforts. Conclusion: this summit should contribute to greater semantic interoperability (in significantly beneficial ways) by showing how to reason across the upper ontologies actually used (and thus to reason across the different sorts of data annotated in their terms)