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A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
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Conversion of KEGG metabolic pathways to SBGN maps including automatic layout
Tobias Czauderna1, Michael Wybrow, Kim Marriott
1Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany. czauderna@ipk-gatersleben.de.
BMC Bioinformatics
|August 20, 2013
Summary
We developed a method to automatically translate Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways into Systems Biology Graphical Notation (SBGN). This ensures SBGN compliance while preserving KEGG pathway recognizability.
Area of Science:
- Systems Biology
- Bioinformatics
- Computational Biology
Background:
- Biologists utilize complex biological network databases like KEGG, which employs unique pathway layouts.
- A new standard, Systems Biology Graphical Notation (SBGN), aims to unify biological map representations.
- Automatic conversion of KEGG pathways to SBGN is challenging due to layout preservation issues.
Purpose of the Study:
- To present a methodology for automatically translating KEGG metabolic pathways into the SBGN format.
- To maintain the integrity and recognizability of original KEGG pathways during conversion.
Main Methods:
- Inferring key properties of KEGG pathway layouts.
- Applying these properties as constraints during the conversion process to SBGN.
- Developing an automatic translation methodology.
Main Results:
- Successful automatic translation of KEGG metabolic pathways to SBGN format.
- Preservation of original KEGG pathway layouts and recognizability within the SBGN format.
- Demonstration of the conversion process and resulting maps.
Conclusions:
- The methodology allows for adherence to SBGN drawing and layout conventions.
- Generated SBGN maps remain clearly identifiable as the original KEGG pathways.
- The article details the conversion steps and provides illustrative examples.
