Author: Peter Karp

The MetaCyc database ( http://metacyc.org) is a collection of more than a thousand metabolic pathways from a wide variety of organisms, collected from the literature by manual curation.

An updated genome-scale reconstruction of the metabolic network in Escherichia coli K-12 MG1655 is presented.

Using the completed V.cholerae genome sequence and PathoLogic software, we created VchoCyc, a pathway-genome database that predicted 171 likely metabolic pathways in the bacterium.

We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers.

Different biological notions of pathways are used in different pathway databases. Those pathway ontologies significantly impact pathway computations.

The Pathway Tools software allows a group of scientists to create, update, and publish on the Web an evolving knowledge resource describing the genome and biochemical networks of the organism.

Pathway Tools supports interrogation and exploration of cellular biochemical networks through the overview diagram and a software component called the Omics Viewer.

MetaCyc contains metabolic pathways, enzymatic reactions, enzymes, chemical compounds, genes and review-level comments.

In conjunction with the Pathway Tools software, MetaCyc can be used to computationally predict the metabolic pathway complement of an annotated genome.

The mission for EcoCyc is to contain both computable descriptions of, and detailed comments describing, all genes, proteins, pathways and molecular interactions in E.coli.