Upper Ontology Summit Wednesday March 15 The BFO perspective Barry Smith Department of Philosophy, University at Buffalo National Center for Ontological Research National Center for Biomedical Ontology

Basic Formal Ontology BFO is a highest-common-denominator upper ontology designed to support interoperability between domain ontologies supporting shared use of scientific research data across disciplinary boundaries BFO used and tested primarily within the biomedical domain; part of a collaborative effort with research groups and consortia supported by the NIH to make clinical trial data and model organism experimental data re-usable when diagnostic criteria or experimental hypotheses change

The core of BFO importance of axioms and definitions distinction between types and instances the acceptance of both continuants and occurrents the distinction between dependent continuants (for example: organisms) and dependent continuants (for example: qualities, functions, roles)

First key distinguishing mark Data are primarily about instances Ontologies are primarily about types Compare A-box / T-box in Description Logics instance-level relations this cell nucleus adjacent_to this cytoplasm type-level relations cell nucleus adjacent_to cytoplasm

Second key distinguishing mark BFO allows quantification not only over instances but also over types (using the same individual variables for each)

BFO is very small It strives to be the highest common factor ontology relative to those upper ontologies which are (1) formally sufficiently robust to support data management needs of high-level scientific research (2) sufficiently broad in scope to support cross-granular and cross-disciplinary alignment of domain ontologies (3) sufficiently commonsensical to attract large numbers of users from the side of domain science

Why should an upper ontology be small? Biologists need an upper ontology if they are to achieve domain ontology alignment. This should be an upper ontology which they can understand and accept They will not accept an upper ontology which embodies an axiomatic treatment of biological types (like monkey, vegetable,...)

Reasons for axiomatization Axiomatization and formal definitions at the top can help bring about advances towards logic- based reasoning when working with very large domain ontologies But: axioms and definitions formulated exclusively in machine-understandable terms will not be used by those developing domain ontologies Hence BFO is maintained in equivalent human- intelligible and machine-intelligible formats

OBO Foundry OBO = Open Biomedical Ontologies Consortium ( 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* Upper ontology of OBO Foundry project = shared common sense of biomedical scientists *see “Relations in Biomedical Ontologies”, Genome Biology, Apr. 2005,

Conclusions We need to distinguish the needs of ontology experts from those of ontology users An upper ontology should be marked not merely by high formal rigor but also by conformity with human common sense