The BioCyc collection of Pathway/Genome Databases (PGDBs) developed by SRI International contains databases for more than 3,000 organisms. Common to these PGDBs is their derivation from the MetaCyc PGDB. MetaCyc contains 1,800 experimentally elucidated metabolic pathways found in 2,200 organisms. The MetaCyc data were curated from 34,000 publications. BioCyc contains a number of tools for analysis of gene expression, proteomics, and metabolomics data. One set of tools enables users to paint omics data onto a zoomable metabolic map diagram, onto individual pathway diagrams, onto a regulatory map diagram, and onto a genome map diagram. Tools for enrichment analysis are also provided, for example, gene sets can be analyzed for statistically over-represented occurrence of genes in Gene Ontology categories, and for over representation of regulatees of known regulators. Metabolite sets can be searched for over-representation of substrates of known metabolic pathways.