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

Clemens Wrzodek1, Andreas Dräger, Andreas Zell

  • 1Center for Bioinformatics Tuebingen, University of Tuebingen, 72076 Tübingen, Germany. clemens.wrzodek@uni-tuebingen.de

Bioinformatics (Oxford, England)
|June 25, 2011
PubMed
Summary

KEGGtranslator is a new application that converts KEGG Markup Language (KGML) pathway files into multiple formats. It enhances pathway data and aids in simulations.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • The KEGG PATHWAY database is a crucial resource for metabolic and nonmetabolic pathways.
  • Pathway data is stored in KEGG Markup Language (KGML), a proprietary XML format.
  • Processing KGML files for other applications requires specialized parsers and translators.

Purpose of the Study:

  • To develop an easy-to-use application for visualizing and converting KGML files.
  • To provide a versatile tool that supports numerous output formats.
  • To augment KGML data with additional information and complete fragmentary reactions for simulations.

Main Methods:

  • Development of KEGGtranslator, a stand-alone Java Web Start application.
  • Implementation of KGML file parsing and conversion capabilities.
  • Integration of features for augmenting pathway data and handling incomplete reactions.

Main Results:

  • KEGGtranslator successfully visualizes and converts KGML files into various formats.
  • The application supports a wider range of output formats compared to existing translators.
  • KEGGtranslator can enrich translated documents with external annotations (e.g., MIRIAM) and complete reaction data.

Conclusions:

  • KEGGtranslator offers a flexible and powerful solution for processing KEGG pathway data.
  • The tool facilitates the use of pathway information in diverse downstream applications and simulations.
  • Enhanced pathway data and support for simulations are key advantages of KEGGtranslator.