Ontology as ethogram: knowledge representation for behavior

P.E. Midford

Ecology and Evolutionary Biology, University of Arizona, Tucson, U.S.A.

 

Artificial Intelligence has, over the past 20 years, developed several approaches to representing knowledge about the common-sense world. The term 'ontology' has been applied to numerous knowledge representation schemes, ranging from controlled vocabularies to more powerful logic-based systems. Several ontologies have already been developed for molecular biology (e.g. EcoCyc [1]) and genomics (e.g. Gene Ontology [2]).

Frame-based ontologies, which were used in this study, represent an intermediate level of representation power. Such ontologies can explicitly represent concepts (e.g. behavior types), individuals (e.g. events) and relations (e.g. type hierarchies or temporal sequencing). An ontology partially defines concepts in relation to existing concepts, providing flexility and reducing the tendency to “pigeon-hole” novel exemplars. Explicit definitions of relationships and their properties can unmask assumptions and may provide a basis for describing evolutionary change.

This study explores ontology-based representations as an alternative to conventional ethograms, using Protege-2000, currently one of the most popular ontology editors. The “frame” paradigm used by Protege-2000 provides an intermediate representation power with a relatively friendly user interface. Protege-2000 also directly supports the use of the ontology as a scheme for a database of events that support the descriptive representation. These events generally link or refer to digitized media.

I will present ontologies developed for a comparative study of courtship in a clade of Habronattus jumping spiders, as well as an earlier ontology based on a published ethogram of loggerhead seaturtle Caretta caretta nesting. Extensions to the Protege-2000 tool, to improve editing and checking of behavioral data, will also be described.

References

  1. Karp, P.D.; Riley, M.; Saier, M.; Paulsen, I.T.; Paley, S.; Pellegrini-Toole, A. (2002). The EcoCyc Database. Nucleic Acids Research, 30(1), 56.
  2. The Gene Ontology Consortium. (2000). Gene Ontology: tool for the unification of biology. Nature Genetics, 25, 25-29.

Paper presented at Measuring Behavior 2002 , 4th International Conference on Methods and Techniques in Behavioral Research, 27-30 August 2002, Amsterdam, The Netherlands

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