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

Ron Caspi, Tomer Altman, Joseph M. Dale, Kate Dreher, Carol A. Fulcher, Fred Gilham, Pallavi Kaipa, Athikkattuvalasu S. Karthikeyan, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Lukas A. Mueller (+6 others)
2009 Nucleic Acids Research  

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https://web.archive.org/web/20180730125628/https://watermark.silverchair.com/gkp875.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAaowggGmBgkqhkiG9w0BBwagggGXMIIBkwIBADCCAYwGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMTrG7TcGi32pzHT0DAgEQgIIBXaCJG635ckmO8mr9rV7C0Tff0KxdTOUXfLRPDW_jBF9Rr2IvBXqTe7JVFiAwaXYbX6OuNTxD_t3gulO93FTc-ykLKZRTEu3ZMPFK_b2e_-89KOhrhMLhK51IJRtleE5jxiCLaALLyTE9Bw92qDPApqjVP9jwhOfwcRdbUMPDd6m8o_NUFMowIVClF9RNcasRsHoRwa8hxYxwrGv8Zpc_9sgGuQSNARrgd67gYs2pjpHwai4jTHW_BtypDjf8-RpDkefDxfJq56entEtvu5HX0PI1Nb_mADJ9zpb0P2nBSI1DPlQASfmgXtT2-VjAcEYyAAiI2K1x7wtrfdTJpmSaTXsIClQSXIn_ujInwRNMuWz2wL9biXO-v0Vy5WsM-TnHvLcALbQh-Zp6UzyFAL29NW1faDg2N4UpiVY4p1hIWZhsk_p3AmoGeSY0NjIrG0-HzG7kQGxjL_NkRI4rRkM

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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
more » ... 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 holefillers. 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 genomerelated information about an organism.
doi:10.1093/nar/gkp875 pmid:19850718 pmcid:PMC2808959 fatcat:3mdlecp47rbszcro7wmgktztqi
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Ron Caspi, Tomer Altman, Joseph M. Dale, Kate Dreher, Carol A. Fulcher, Fred Gilham, Pallavi Kaipa, Athikkattuvalasu S. Karthikeyan, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Lukas A. Mueller, Suzanne Paley, Liviu Popescu, Anuradha Pujar, Alexander G. Shearer, Peifen Zhang, Peter D. Karp. "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases." Nucleic Acids Research 38.suppl_1 (2009) D473-D479