Pathway Tools provides a comprehensive environment for manipulating molecular regulatory interactions that integrates regulatory data with an organism’s genome and metabolic network. Curated collections of regulatory data authored using Pathway Tools are available for Escherichia coli, Bacillus subtilis, and Shewanella oneidensis.
The BioCyc database collection at BioCyc.org integrates genome and cellular network information for more than 1,100 organisms.
Pathway Tools is a production-quality software environment for creating a type of model-organism database called a Pathway/Genome Database (PGDB).
The annotation of the Escherichia coli K-12 genome in the EcoCyc database is one of the most accurate, complete and multidimensional genome annotations.
Pathway Tools supports interrogation and exploration of cellular biochemical networks through the overview diagram and a software component called the Omics Viewer.
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.
MetaCyc is a database of metabolic pathways and enzymes located at http://MetaCyc.org/. Its goal is to serve as a metabolic encyclopedia, containing a collection of non-redundant pathways central to small molecule metabolism, which have been reported in the experimental literature. Most of the pathways in MetaCyc occur in microorganisms and plants, although animal pathways are also represented. MetaCyc contains metabolic pathways, enzymatic reactions, enzymes, chemical compounds, genes and review-level comments. Enzyme information includes substrate specificity, kinetic properties, activators, inhibitors, cofactor requirements and links to sequence and structure databases.
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.
We describe multiple methods for accessing and querying the complex and integrated cellular data in the BioCyc family of databases.
This paper presents an ontology for encoding the type of support and the degree of support for DB assertions, and for encoding the literature source in which that support is reported.
In the past 2 years the data content and the Pathway Tools software used to query, visualize and edit MetaCyc have been expanded significantly. These enhancements are described in this paper.
A Pathway/Genome Database for Helicobacter pylori is available at URL BioCyc.org. The database integrates the full genome of H. pylori with its computationally predicted metabolic pathways. HpyCyc is part of a larger collection of Pathway/Genome Databases called the BioCyc collection. The BioCyc website provides a wide array of query and visualization tools for HpyCyc, including a genome browser, pathway displays, and a visualization of the complete metabolic map of H. pylori on which gene expression data can be superimposed.
We seek to determine the accuracy of computational methods for predicting metabolic pathways in sequenced genomes, and to understand the contributions of both the prediction algorithms, and the reference pathway databases used by those algorithms, to the prediction accuracy.
Bioinformatics requires reusable software tools for creating model-organism databases (MODs). The Pathway Tools is a reusable, production-quality software environment for creating a Pathway/Genome Database (PGDB).