We have constructed a natural products database, "RIKEN Natural Products Encyclopedia (RIKEN NPEdia)", as an informatics part of chemical resource bank, "the RIKEN Natural Products Depository (RIKEN NPDepo)". Approximately 25,000 compound data are now listed in NPEdia, some of which were transferred from "KNApSAcK", a secondary metabolites database constructed by Prof. Kanaya and his colleagues (http://kanaya.aist-nara.ac.jp/KNApSAcK/, http://prime.psc.riken.jp/ (mirror site)). Compounds listed in NPEdia are mainly secondary metabolites isolated from actinomycetes, fungi, plants and other organisms. Each compound data consists of molecular structure, origin, and physico-chemical and biological properties. MOL files can be also downloaded. Ultra-Violet, MS/MS and NMR spectra will also be included in the near future. This database involves three functions: (1) searching for compounds, (2) registering compound data and (3) co-operating in compound-order system. We are now trying to integrate metabolites with metabolic pathway maps, protein-protein interaction maps, and chemical genomics maps (relationship between metabolic pathways and small molecules "bioprobes" interacting them). We think NPEdia should be a useful database friendly to researchers in various research fields. The details and latest news about NPEdia are described on the website (http://npd.riken.jp/).