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Updated: May 13, 2026
08:01
A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
Precise generation of systems biology models from KEGG pathways
Clemens Wrzodek1, Finja Büchel, Manuel Ruff
1Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany. clemens.wrzodek@uni-tuebingen.de
BMC Systems Biology
|February 26, 2013
Summary
A new method precisely converts KEGG pathways into accurate metabolic and signaling models using Systems Biology Markup Language (SBML) and BioPAX formats. This approach ensures complete stoichiometric reactions and extensive cross-references for robust systems biology applications.
Area of Science:
- Systems biology
- Bioinformatics
- Computational biology
Background:
- KEGG PATHWAY database offers extensive biological pathways linked to other KEGG resources.
- KGML format prioritizes visualization, often omitting crucial details for direct systems biology modeling.
- Direct conversion of KGML to models can result in incomplete and inaccurate systems biology representations.
Purpose of the Study:
- To develop a precise method for converting KEGG pathways into standardized SBML and BioPAX formats.
- To address limitations of KGML by correcting errors and completing pathway information.
- To facilitate the creation of accurate metabolic and signaling models from pathway data.
Main Methods:
- Processing and converting KEGG pathways using a novel method.
- Correcting invalid or incomplete KGML content.
- Generating complete stoichiometric reactions for metabolic models.
- Translating pathway relations into signaling models.
- Augmenting models with cross-references to external databases (Entrez Gene, UniProt, etc.).
- Comparing existing KEGG conversion tools.
Main Results:
- Developed a method to convert KEGG pathways into SBML (Levels 2 and 3) and BioPAX (Levels 2 and 3) formats.
- Achieved lossless conversion to BioPAX.
- Demonstrated that lossless conversion to SBML requires SBML Level 3, including extensions for qualitative models and groups.
- Created initial models with valid SBML/BioPAX code and numerous cross-references.
Conclusions:
- The proposed method uniquely enables the construction of accurate BioPAX and SBML signaling models from KEGG.
- This approach is the only one capable of constructing accurate metabolic models with correct stoichiometry from KEGG pathways.
- The generated initial models provide a solid foundation for advanced systems biology modeling and analysis.
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