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

• DOI: 10.1093/bioinformatics/btr377
• Publication Date: 2011-06-24T01:56:40Z
• Authors: Clemens Wrzodek; Andreas Dräger; Andreas Zell
• Keywords: KEGG; Scope (computer science)

Abstract Summary: The KEGG PATHWAY database provides a widely used service for metabolic and nonmetabolic pathways. It contains manually drawn pathway maps with information about the genes, reactions relations contained therein. To store these pathways, uses KGML, proprietary XML-format. Parsers translators are needed to process usage in other applications algorithms. We have developed KEGGtranslator, an easy-to-use stand-alone application that can visualize convert KGML formatted XML-files into multiple output formats. Unlike translators, KEGGtranslator supports plethora of formats, is able augment translated documents (e.g. MIRIAM annotations) beyond scope document, amends missing components fragmentary within allow simulations on those. Availability: freely available as Java™ Web Start download at http://www.cogsys.cs.uni-tuebingen.de/software/KEGGtranslator/. files be downloaded from application. Contact: [e-mail] Supplementary information: data Bioinformatics online.