Bioinformatics publications

New developments include atom mappings in reactions, a new representation of glycan degradation pathways, improved compound structure display, better coverage of enzyme kinetic data, enhancements of the Web Groups functionality...

Each BioCyc PGDB contains the predicted metabolic network of one organism, including metabolic pathways, enzymes, metabolites and reactions predicted by the Pathway Tools software using MetaCyc as a reference database.

Gene Ontology (GO) is one of the most successful systems for classifying biological function. Although GO is widely used for eukaryotic genomics, it has not yet been widely used for…

The EcoCyc database integrates information about the E. coli genome, its metabolic pathways, and its regulatory network. EcoCyc is in use by scientists from a variety of disciplines.

BioWarehouse is an open-source project for integrating bioinformatics databases within a relational database warehouse. It has multiple databases can be queried together within a single common schema.

The annotation of the Escherichia coli K-12 genome in the EcoCyc database is one of the most accurate, complete and multidimensional genome annotations.

Genome-context methods have proved useful in providing clues about functional annotations for many proteins. They detect many biological types of functional associations, and do not identify which type of functional…

Here we present a follow-up literature-based survey involving a statistically significant sample of such "orphan" activities.

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.

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