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Bioinformatics Advance Access originally published online on December 1, 2006
Bioinformatics 2007 23(3):344-350; doi:10.1093/bioinformatics/btl611
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Dynamic exploration and editing of KEGG pathway diagrams

Christian Klukas and Falk Schreiber *

Leibniz Institute of Plant Genetics and Crop Plant Research Corrensstrasse 3, 06466 Gatersleben, Germany

*To whom correspondence should be addressed.


  Abstract

Motivation: The Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway database is a very valuable information resource for researchers in the fields of life sciences. It contains metabolic and regulatory processes in the form of wiring diagrams, which can be used for browsing and information retrieval as well as a base for modeling and simulation. Thus it helps in understanding biological processes and higher-order functions of biological systems.

Currently the KEGG website uses semi-static visualizations for the presentation and navigation of its pathway information. While this visualization style offers a good pathway presentation and navigation, it does not provide some of the possibilities related to dynamic visualizations, most importantly, the creation and visualization of user-specific pathways.

Results: This paper presents methods for the dynamic visualization, interactive navigation and editing of KEGG pathway diagrams. These diagrams, given as KEGG Markup Language (KGML) files, can be visually explored using novel approaches combining semi-static and dynamic visualization, but also edited or even newly created and then exported into KGML files.

Availability: KGML-ED, a program implementing the presented methods, is available free of charge to the scientific community at http://kgml-ed.ipk-gatersleben.de

Contact: schreibe{at}ipk-gatersleben.de

Associate Editor: Alvis Brazma

Received on August 1, 2006; revised on November 3, 2006; accepted on November 24, 2006

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[Abstract] [Full Text] [PDF]


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