Upper Ontology Summit The BFO perspective

1. Upper Ontology Summit The BFO perspective Barry Smith Department of Philosophy, University at Buffalo National Center for Ontological Research National Center for Biomedical Ontology

2. Basic Formal Ontology • Basic Formal Ontology is a highest-common denominator upper ontology designed to support interoperability between machines, disciplines and human beings in natural science research • BFO used and tested primarily within the biomedical domain; is part of an collaborative effort with research groups and consortia supported by the National Institutes of Health to make clinical trial and model organism experimental data re-usable when diagnostic criteria or experimental hypotheses change

3. The core of BFO • importance of axioms and definitions • distinction between types and instances • the acceptance of both continuants and occurrents • the acceptance of both independent continuants (for example: organisms) and dependent continuants (for example: qualities, functions, roles) • importance of the distinction between instance-level relations, for example: • this cell nucleus adjacent_to this cytoplasm level • and type-level relations • cell nucleus adjacent_to cytoplasm • (adjacency, continuity, simultaneity are not symmetric on the level of types)

4. Relation to DOLCE • BFO and DOLCE have common roots, and are currently subject to an effort towards unification • Differences in treatment of time, space and qualities • BFO is a strictly upper ontology, leaving the treatment of domain-specific types to domain ontologies • DOLCE incorporates domain-ontological notions of various sorts

5. Points of Agreement • We desire semantic interoperability. • We agree that a mere taxonomy is insufficient for that. • We agree that axioms are an indispensable part of creating semantic interoperability.

6. BFO is very small • It strives to be the highest common factor of those upper ontologies which are • (1) formally sufficiently robust and to support high-level scientific research • (2) sufficiently broad in scope to support cross-granularity alignment of domain ontologies • (3) sufficiently commonsensical to attract large numbers of users from the side of domain science • Biologists will not accept an upper ontology which embodies an axiomatic treatment of types like monkey • Biologists will not accept an upper ontology which does not include both 3D and 4D entities

7. Points of Agreement • We desire semantic interoperability. • We agree that a mere taxonomy is insufficient for that. • We agree that axioms are an indispensable part of creating semantic interoperability. • Axiomatization at the top can help bring about coherent advances where one needs to work with very large domain ontologies, some with million+ terms, very few of which have been subjected to coherent formal treatment

8. OBO Foundry • OBO = Open Biomedical Ontologies Consortium (http://obo.sourceforge.net) • OBO Foundry = a subset of OBO ontologies which agree in advance to accept a common set of principles designed to assure formal robustness and interoperability* • BFO is the upper ontology of the OBO Foundry project • *see “Relations in Biomedical Ontologies”, Genome Biology, Apr. 2005.

9. The biomedical research groups within the OBO Foundry use a variety of (more or less) formal approaches • Hence BFO itself needs at this stage to be maintained in different mutually compatible formats – intelligible to both human beings and machines – in order to support their work • Human friendly upper ontology can support wide use, fewer errors in use, openness to prospective users – and openness to other upper ontologies