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. 2008 Jan;36(Database issue):D623-31.
doi: 10.1093/nar/gkm900. Epub 2007 Oct 27.

The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

Ron Caspi  1 , Hartmut Foerster, Carol A Fulcher, Pallavi Kaipa, Markus Krummenacker, Mario Latendresse, Suzanne Paley, Seung Y Rhee, Alexander G Shearer, Christophe Tissier, Thomas C Walk, Peifen Zhang, Peter D Karp
Affiliations

The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

Ron Caspi et al. Nucleic Acids Res. 2008 Jan.

Abstract

MetaCyc (MetaCyc.org) is a universal database of metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are curated from the primary scientific literature, and are experimentally determined small-molecule metabolic pathways. Each reaction in a MetaCyc pathway is annotated with one or more well-characterized enzymes. Because MetaCyc contains only experimentally elucidated knowledge, it provides a uniquely high-quality resource for metabolic pathways and enzymes. BioCyc (BioCyc.org) is a collection of more than 350 organism-specific Pathway/Genome Databases (PGDBs). 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. BioCyc PGDBs also contain predicted operons and predicted pathway hole fillers-predictions of which enzymes may catalyze pathway reactions that have not been assigned to an enzyme. The BioCyc website offers many tools for computational analysis of PGDBs, including comparative analysis and analysis of omics data in a pathway context. The BioCyc PGDBs generated by SRI are offered for adoption by any interested party for the ongoing integration of metabolic and genome-related information about an organism.

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Figures

Figure 1.
Figure 1.
An example of a pathway in MetaCyc. Pathways can be displayed at varying levels of detail. This pathway display depicts an intermediate level of detail including enzymes, EC numbers, genes and chemical structures of the main compounds. Notice the green arrow at the bottom of the pathway, which provides a hyperlink to a related downstream pathway.
Figure 2.
Figure 2.
The regulatory overview. The diagram is composed of three nested ellipses. The innermost ellipse comprises genes that are regulating other genes, but that are not regulated by any genes. The middle ellipse comprises genes that are both regulators and regulatees (= regulated by some entity), and the outermost ellipse comprises genes that are regulated, but do not regulate. The triangles that extend outward from the outer ellipse are collections of many genes that share the same set of regulator genes-although genes within a triangle may respond to those regulators in different ways. They are drawn within triangles simply to keep the size of the outer ellipse manageable.
Figure 3.
Figure 3.
The genome overview. This tool allows the user to view the full chromosome of an organism on a single-page diagram, and to paint expression or other omics data onto it.
See this image and copyright information in PMC

References

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