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The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/ genome databases (2012)
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| Venue: | Nucleic Acids Res |
| Citations: | 403 - 15 self |
BibTeX
@ARTICLE{Caspi12themetacyc,
author = {Ron Caspi and Tomer Altman and Richard Billington and Kate Dreher and Hartmut Foerster and Carol A. Fulcher and Timothy A. Holl and Ingrid M. Keseler and Anamika Kothari and Aya Kubo and Markus Krummenacker and Mario Latendresse and Lukas A. Mueller and Quang Ong and Suzanne Paley and Pallavi Subhraveti and Daniel S. Weaver and Deepika Weerasinghe and Peifen Zhang and Peter D. Karp},
title = {The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/ genome databases},
journal = {Nucleic Acids Res},
year = {2012},
pages = {742--753}
}
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Abstract
The MetaCyc database (MetaCyc.org) is a compre-hensive and freely accessible database describing metabolic pathways and enzymes from all domains of life. MetaCyc pathways are experimentally determined, mostly small-molecule metabolic pathways and are curated from the primary scien-tific literature. MetaCyc contains>2100 pathways derived from>37000 publications, and is the largest curated collection of metabolic pathways currently available. BioCyc (BioCyc.org) is a collec-tion of>3000 organism-specific Pathway/Genome Databases (PGDBs), each containing the full genome and predicted metabolic network of one organism, including metabolites, enzymes, reac-tions, metabolic pathways, predicted operons, transport systems and pathway-hole fillers. Additions to BioCyc over the past 2 years include YeastCyc, a PGDB for Saccharomyces cerevisiae, and 891 new genomes from the Human Microbiome Project. The BioCyc Web site offers a variety of tools for querying and analysis of PGDBs, including Omics Viewers and tools for comparative analysis. 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 functional-ity, improvements to the Omics viewers, a new representation of the Enzyme Commission system and, for the desktop version of the software, the ability to save display states.
