Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2011 Aug 15;27(16):2314-5.
doi: 10.1093/bioinformatics/btr377. Epub 2011 Jun 23.

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

Clemens Wrzodek  1 , Andreas Dräger, Andreas Zell
Affiliations

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

Clemens Wrzodek et al. Bioinformatics. .

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 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(™) Web Start application and for download at http://www.cogsys.cs.uni-tuebingen.de/software/KEGGtranslator/. KGML files can be downloaded from within the application.

Contact: clemens.wrzodek@uni-tuebingen.de

Supplementary information: Supplementary data are available at Bioinformatics online.

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
(A) Screenshot of a translated GraphML pathway in KEGGtranslator. (B) The need for autocompleting reactions: the upper half shows the KGML-file with only one substrate and product. On the lower half, the complete reaction equation is shown. As one can see, one substrate and product is missing in the XML-document.
See this image and copyright information in PMC

References

    1. Dräger A., et al. JSBML: a flexible and entirely Java-based library for working with SBML. Bioinformatics. 2011 in press. - PMC - PubMed
    1. Dräger A., et al. SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks. BMC Syst. Biol. 2008;2:39. - PMC - PubMed
    1. Dräger A., et al. SBML2LaTeX: conversion of SBML files into human-readable reports. Bioinformatics. 2009;25:1455–1456. - PMC - PubMed
    1. Funahashi A., et al. 8th Annual International Conference on Research in Computational Molecular Biology. 2004. Converting KEGG pathway database to SBML.
    1. Heinrich R., Schuster S. The Regulation of Cellular Systems. 2. Berlin: Springer; 2006.

Publication types