The RiboWeb system is an online data resource for the ribosome, a vital cellular apparatus responsible for building proteins in all organisms. RiboWeb contains a large knowledge base of relevant published data and computational modules that can process this data to test hypotheses about the ribosome's structure. The system uses four principle ontologies to organize its knowledge. The first models molecules and processes relevant to molecular biology. The second describes biological data that has been collected about the ribosome and their key features and relationships. The third represents scientific publications and their key attributes. Finally, RiboWeb uses an ontology of the types of computations that it can perform. This declarative representation of computational capabilities allows explicit reasoning about possible actions and sequences of actions.