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The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
Open accessAbstract
The MetaCyc database (MetaCyc.org) is 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. With more than 1400 pathways, MetaCyc is the largest collection of metabolic pathways currently available. Pathways reactions are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes, and literature citations. BioCyc (BioCyc.org) is a collection of more than 500 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, consists of metabolites, enzymes, reactions and metabolic pathways. BioCyc PGDBs also contain additional features, such as predicted operons, transport systems, and pathway hole-fillers. The BioCyc Web site offers several tools for the analysis of the PGDBs, including Omics Viewers that enable visualization of omics datasets on two different genome-scale diagrams and tools for comparative analysis. The BioCyc PGDBs generated by SRI are offered for adoption by any party interested in curation of metabolic, regulatory, and genome-related information about an organism.
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Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology
Karp, P. D., Paley, S. M., Krummenacker, M., Latendresse, M., Dale, J. M., Lee, T. J., Kaipa, P., Gilham, F., Spaulding, A., Popescu, L., et al. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbp043 · Cited by 694
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Metadata
- Authors
- Caspi, R., Altman, T., Dale, J. M., Dreher, K., Fulcher, C. A., Gilham, F., Kaipa, P., Karthikeyan, A. S., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L. A., Paley, S., Popescu, L., Pujar, A., Shearer, A. G., Zhang, P., & Karp, P. D.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-10-22
- Volume
- 38
- Issue
- suppl_1
- Pages
- D473-D479
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W4233060585
- Cited by
- 483
- References
- 2
- FWCI
- 25.81
- Type
- journal article
- Language
- en
- Open access
- gold
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- Caspi, R., Altman, T., Dale, J. M., Dreher, K., Fulcher, C. A., Gilham, F., Kaipa, P., Karthikeyan, A. S., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L. A., Paley, S., Popescu, L., Pujar, A., Shearer, A. G., Zhang, P., & Karp, P. D. (2010). 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/gkp875
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
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.
