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The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

Open access
Caspi, R., Altman, T., Dreher, K., Fulcher, C. A., Subhraveti, P., Keseler, I. M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L. A., Ong, Q., Paley, S., Pujar, A., Shearer, A. G., Travers, M., Weerasinghe, D., Zhang, P., Karp, P. D.·2012·Nucleic Acids Research
DOI 10.1093/nar/gkr1014
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Abstract

The MetaCyc database (http://metacyc.org/) provides a comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. MetaCyc contains more than 1800 pathways derived from more than 30,000 publications, and is the largest curated collection of metabolic pathways currently available. Most reactions in MetaCyc pathways are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes and literature citations. BioCyc (http://biocyc.org/) is a collection of more than 1700 organism-specific Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the full genome and predicted metabolic network of one organism. The network, which is predicted by the Pathway Tools software using MetaCyc as a reference database, consists of metabolites, enzymes, reactions and metabolic pathways. BioCyc PGDBs contain additional features, including predicted operons, transport systems and pathway-hole fillers. The BioCyc website and Pathway Tools software offer many tools for querying and analysis of PGDBs, including Omics Viewers and comparative analysis. New developments include a zoomable web interface for diagrams; flux-balance analysis model generation from PGDBs; web services; and a new tool called Web Groups.

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Metadata

Authors
Caspi, R., Altman, T., Dreher, K., Fulcher, C. A., Subhraveti, P., Keseler, I. M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L. A., Ong, Q., Paley, S., Pujar, A., Shearer, A. G., Travers, M., Weerasinghe, D., Zhang, P., & Karp, P. D.
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2011-11-18
Volume
40
Issue
D1
Pages
D742-D753
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkr1014
OpenAlex
W4237293127
Cited by
601
References
2
FWCI
30.80
Type
journal article
Language
en
Open access
gold
Licence
creativecommons.org/licenses/by-nc/3.0 (vor, 2002 d)

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CoChat. (2026). Citation check: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. https://app.cochat.ai/papers/10.1093/nar/gkr1014
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Caspi, R., Altman, T., Dreher, K., Fulcher, C. A., Subhraveti, P., Keseler, I. M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L. A., Ong, Q., Paley, S., Pujar, A., Shearer, A. G., Travers, M., Weerasinghe, D., Zhang, P., & Karp, P. D. (2012). The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Research. https://doi.org/10.1093/nar/gkr1014

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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.