From GENIA to BioTop -- Towards a top-level ontology for biology

Stefan Schulz, Elena Beisswanger, Udo Hahn, Joachim Wermter, Holger Stenzhorn and Anand Kumar

International Conference on Formal Ontology in Information Systems (FOIS 2006)
Baltimore, Maryland (USA), November 9-11, 2006

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Abstract

The increasing need for ontological support in the life sciences is being generally acknowledged, but up until now, the development of biological upper level ontologies have mainly been purpose-driven. An example is the GENIA ontology, covering biological continuants, which has mainly been devised for corpus annotation in a text mining context.

As an alternative, we here present BioTop, an upper ontology of physical continuants in the domain of biology, with a coverage similar to the GENIA ontology. We report on design specifications and modeling decisions based upon formal ontology principles. A major desideratum was to describe the classes in terms of both necessary and sufficient properties. This could be accomplished for 85 out of 146 classes. Conscious of the trade-off between expressivity and computational feasibility, we opted for constraining our description language to OWL-DL, with the advantage of using a terminological classifier for maintaining consistency, as a major heuristic support in the ontology building process.

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