Abstract: A pathway/genome database (DB) integrates
information about the genes,
gene products, and biochemical pathways of an organism. For example, the
EcoCyc DB describes the full genome and metabolic-pathway complement of E.
coli. The Pathway Tools is a Common Lisp software system that includes
algorithms for interrogation, visualization,
editing, and WWW publishing of pathway/genome DBs. It also includes tools
for pathway visualization of gene-expression data, for comparative analysis
of metabolic networks, and for prediction of the metabolic network of an
organism. The Pathway Tools has been applied
to 15 organisms by researchers at SRI and elsewhere, and is a mature, reusable
environment for creating new model-organism databases.