http://ontologist.com

Upper Ontology SummitTuesday March 14

The BFO perspective

Barry SmithDepartment of Philosophy, University at Buffalo

National Center for Ontological ResearchNational Center for Biomedical Ontology

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

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

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?

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

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)

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)

http://ontologist.com

Upper ontologies require usersWe 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

http://ontologist.com

The methodology of annotationsScientists 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

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

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)