The Pathway Tools project at SRI aims to build a software environment that enables scientists to build declarative databases that store biological theories in forms that are accessible to human scientists, and to automated reasoners. We are developing a platform for symbolic systems biology -- the application of symbolic reasoning methods to the complete biochemical network of a cell. Among the components of Pathway Tools are: a large biological ontology that facilitates the capture of complex biological knowledge with high fidelity; a set of inference modules for inferring new layers of biological information above an annotated genome, such as the metabolic pathway map of an organism; editing tools that allow scientists to interactively refine and curate these databases; and visualization tools that support web publishing, querying, and analyses of these data.

This talk will provide an overview of Pathway Tools and of the BioCyc collection of pathway/genome databases developed at SRI using Pathway Tools. The BioCyc collection includes the EcoCyc DB, which describes the full genome and metabolic network of the bacterium E. coli, and a large portion of its genetic network. The talk will describe in more detail algorithms for inference of metabolic networks, and for determining the consistency of the metabolic network of an organism with its growth-media requirements, implemented using a production system.