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Bioinformatics. 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.

Author information

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

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.

PMID:
21700675
PMCID:
PMC3150042
DOI:
10.1093/bioinformatics/btr377
[Indexed for MEDLINE]
Free PMC Article
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