Dynamic exploration and editing of KEGG pathway diagrams

Christian Klukas, Falk Schreiber

Research output: Contribution to journalArticleResearchpeer-review

55 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)344-350
Number of pages7
JournalBioinformatics
Volume23
Issue number3
DOIs
Publication statusPublished - 1 Feb 2007
Externally publishedYes

Cite this