The increasing need for advanced ontology-based knowledge management in the life sciences is generally being acknowledged but, up until now, the development of biological ontologies lacks adherence to foundational principles of ontology design. This is particularly true of so-called upper-level ontologies such as the GENIA ontology which covers biological continuants and has mainly been devised for corpus annotation in a text mining context. As an alternative, we introduce 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 for BIOTOP which are based upon formal ontology principles. As a major desideratum, these continuants are described in terms of necessary and sufficient conditions. We accomplished this goal for 85 out of the 146 existing GENIA classes. We use OWL-DL as a formal knowledge representation language and may thus use a terminological reasoner for classification in order to check and maintain consistency during the ontology engineering phase.