KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats

Summary: The KEGG PATHWAY database provides a widely used service for metabolic and non-metabolic pathways. It contains manu-ally drawn pathway maps with information about the genes, reactions and relations contained therein. To store these pathways, KEGG uses KGML, a proprietary XML-format. Parsers and translators are nee-ded to process the pathway maps for usage in other applications and algorithms. We have developed KEGGtranslator, an easy-to-use stand-alone application that can visualize and convert KGML formatted XML-files into multiple output formats. Unlike other translators, KEGGtranslator supports a plethora of output formats, is able to augment the infor-mation in translated documents (e.g., MIRIAM annotations) beyond the scope of the KGML document, and amends missing components to fragmentary reactions within the pathway to allow simulations on those. Availability: KEGGtranslator is freely available as a JavaTM Web Start application and for download a