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 manually 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 needed 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 information 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 Java(TM)Web Start application and for download at http://www.cogsys.cs.unituebingen.de/software/KEGGtranslator/. KGML files can be downloaded within the application or manually from ftp://ftp.genome.jp/pub/kegg/xml/kgml. CONTACT: clemens.wrzodek@uni-tuebingen.de.


Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes, Showcase Steatosis

Bioinformatics 27(16): 2314-5
25th Jun 2011

Clemens Wrzodek, Andreas Dräger, Andreas Zell

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[Andreas Dräger] [Andreas Zell]

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Cell and Intercellular
Views: 2574
  • Created: 30th Jun 2011 at 08:35
  • Last updated: 24th Oct 2013 at 16:18

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