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

Abstract

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.

Figure 1.

An example of a pathway showing omics data pop-ups. Pathways can be displayed at varying levels of detail, and this pathway’s display depicts an intermediate level of detail including enzymes, EC numbers and genes, but no chemical structures. Notice the green arrows at the top of the pathway, which provide hyperlinks to related upstream pathways. After an omics dataset has been uploaded, the user can easily add data pop-ups to the pathway diagram displaying the omics data for genes or metabolites. The user can select from heat map, bar graph or plot representation. Multiple time points are supported.

Figure 2.

The omics viewers enable visualization of omics datasets on genome-scale diagrams. The background of this figure shows part of the cellular overview, with gene transcription data superimposed over the enzymatic reactions that are catalyzed by the enzymes encoded by the assayed genes. By clicking on a single pathway within the diagram, the user can open a pop-up window that shows the pathway along with the omics data in full scale. The numbers next to gene names indicate the value of the omics data. The colors provide another quantitative indication (for more information, see http://biocyc.org/ov-expr.shtml). When multiple enzymes are known to catalyze the same reaction, multiple, color-coded lines are displayed for that reaction, each describing one gene/enzyme.