KEGGtranslator

visualizing and converting the KEGG PATHWAY database to various formats

Clemens Wrzodek, Andreas Dräger, and Andreas Zell

Center for Bioinformatics Tübingen (ZBIT), Germany




Start KEGGtranslator:
You may start KEGGtranslator directly here as Java webstart application on almost every operating system, or you can download a stand-alone version as runnable JAR file in our downloads section.


Short description:
Nowadays, the KEGG PATHWAY database provides a widely used service for pathway-based information. It contains manually drawn pathway maps with information about the genes, reactions and relations contained therein. To store these pathways, KEGG uses an own XML-format (called “KGML”). Parsers and translators are needed to process the pathway maps for usage in other applications and algorithms.
We have developed KEGGtranslator, which is 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. KEGGtranslator converts KEGG files (KGML formatted XML-files) to SBML, BioPAX, SIF, SBGN, SBML-qual, GML, GraphML, JPG, GIF, LaTeX, etc.
KEGG pathways can be obtained from within the application.


Please cite KEGGtranslator


info
Novel publication We have published a new paper describing in detail the methodology behind KEGGtranslator. Please see and cite "Clemens Wrzodek, Finja Büchel, Andreas Dräger, Manuel Ruff, and Andreas Zell. Precise generation of systems biology models from KEGG pathways. BMC Systems Biology, 7(1):15, January 2013." [ details | link ]   -   (wrzodek - 2013-02-21 14:05)

Release 2.3.0: IMPORTANT UPDATE. Version 2.3 has been released. Due to changes from KEGG, the old KEGGtranslator versions stopped working. This release fixes those issues. You can view the release notes or directly head to the downloads section.   -   (wrzodek - 2013-01-10 13:25)

Release 2.2.0: Updated version with many improvements. Version 2.2 has been released. You can view the release notes or directly head to the downloads section.   -   (wrzodek - 2012-11-12 13:25)

Release 2.0.1: Fixed BioPAX and SBGN outputs. Version 2.0 had serious issues, because the required libraries for BioPAX and SBGN were not included in the jar. This Version now includes all required libraries.   -   (wrzodek - 2012-07-24 09:48)

Release 2.0: KEGGtranslator is now available in the 2.0 release. Massive changes have been performed on the appplication and the algorithms behind. BioPAX is now supported, SBML is now supported as Level 3, including various extensions that also allow for handling relations in KEGG signaling pathway, and many more. See the release notes for what has changed or download KEGGtranslator directly from the downloads section.   -   (wrzodek - 2012-06-04 14:28)

Use microarray data with KEGG pathways: We just released InCroMAP, which includes KEGGtranslator and is able to perform pathway enrichments and visualizations of various microarray data types in KEGG pathways.   -   (wrzodek - 2012-05-04 12:38)

Announcement: KEGGtranslator is soon released in version 2.0. It is then a visualizer and converter for KEGG, SBGN, BioPAX (level 2 and level 3), GraphML, GML, SBML level 2 and level 3, including the qualitative models (qual), groups and layout extensions. Therefore, KEGG2BioPAX, KEGG2SBML, KEGG2SBML_QUAL (KGML2BioPAX, KGML2SBML, KGML2SBML_QUAL) and many more conversions are possible.
Register here to be notified of the upcoming release.   -   (wrzodek - 2012-04-26 09:10)

Release 1.2: KEGGtranslator is now available in the 1.2 release. See the release notes for what has changed or download KEGGtranslator directly from the downloads section.   -   (wrzodek - 2011-07-04 16:47)

Please cite: Clemens Wrzodek, Andreas Dräger, and Andreas Zell. KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats. Bioinformatics, June 2011. [ DOI | details ] (draeger - 2011-06-20 7:50)

FAQ: we have created an initial FAQ.  -   (wrzodek - 2011-05-12 15:34)

Javadoc: a Javadoc, together with examples of how to use the JAR in your own applications is now available here.  -   (wrzodek - 2011-05-12 14:56)

First Release: Launch the application or download a stand-alone version as runnable JAR file.  -   (wrzodek - 2011-01-19 09:23)

KEGG2SBML: KEGGtranslator has been improved to also support KGML2SBML conversion, based on the JSBML library.   -   (wrzodek - 2010-09-12 16:56)

KEGG2GraphML: The first version of KEGGtranslator has been implemented, converting KGML files to GraphML, GML and other graphics based formats.   -   (wrzodek - 2010-02-16 13:02)



This project is promoted by:

BMBF NGFN ZBIT