BMC Bioinformatics. 2009 Oct 08;10:324. doi: 10.1186/1471-2105-10-324.

KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database.

BMC bioinformatics

Konstantinos Moutselos, Ioannis Kanaris, Aristotelis Chatziioannou, Ilias Maglogiannis, Fragiskos N Kolisis

PMID: 19814801 PMCID: PMC2764712 DOI: 10.1186/1471-2105-10-324

Abstract

BACKGROUND: The KEGG Pathway database is a valuable collection of metabolic pathway maps. Nevertheless, the production of simulation capable metabolic networks from KEGG Pathway data is a challenging complicated work, regardless the already developed tools for this scope. Originally used for illustration purposes, KEGG Pathways through KGML (KEGG Markup Language) files, can provide complete reaction sets and introduce species versioning, which offers advantages for the scope of cellular metabolism simulation modelling. In this project, KEGGconverter is described, implemented also as a web-based application, which uses as source KGML files, in order to construct integrated pathway SBML models fully functional for simulation purposes.

RESULTS: A case study of the integration of six human metabolic pathways from KEGG depicts the ability of KEGGconverter to automatically produce merged and converted to SBML fully functional pathway models, enhanced with default kinetics. The suitability of the developed tool is demonstrated through a comparison with other state-of-the art relevant software tools for the same data fusion and conversion tasks, thus illustrating the problems and the relevant workflows. Moreover, KEGGconverter permits the inclusion of additional reactions in the resulting model which represent flux cross-talk with neighbouring pathways, providing in this way improved simulative accuracy. These additional reactions are introduced by exploiting relevant semantic information for the elements of the KEGG Pathways database. The architecture and functionalities of the web-based application are presented.

CONCLUSION: KEGGconverter is capable of producing integrated analogues of metabolic pathways appropriate for simulation tasks, by inputting only KGML files. The web application acts as a user friendly shell which transparently enables the automated biochemically correct pathway merging, conversion to SBML format, proper renaming of the species, and insertion of default kinetic properties for the pertaining reactions. The tool is available at: http://www.grissom.gr/keggconverter.

References

1. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D354-7 - PubMed
2. IEEE/ACM Trans Comput Biol Bioinform. 2008 Oct-Dec;5(4):594-617 - PubMed
3. BMC Bioinformatics. 2006 Mar 06;7:109 - PubMed
4. Pac Symp Biocomput. 2002;:450-61 - PubMed
5. Nat Biotechnol. 2005 Dec;23(12):1509-15 - PubMed
6. BMC Bioinformatics. 2007 Mar 06;8:79 - PubMed
7. Bioinformatics. 2007 Feb 1;23(3):344-50 - PubMed
8. Nucleic Acids Res. 2000 Jan 1;28(1):27-30 - PubMed
9. Bioinformatics. 2003 Mar 1;19(4):524-31 - PubMed
10. Bioinformatics. 2008 Mar 15;24(6):880-1 - PubMed
11. Brief Bioinform. 2008 Jul;9(4):317-25 - PubMed
12. Bioinformatics. 2009 Jun 1;25(11):1470-1 - PubMed
13. BMC Syst Biol. 2008 Apr 30;2:39 - PubMed

MeSH terms

• Computational Biology / methods
• Databases, Factual*
• Internet*
• Metabolic Networks and Pathways / genetics
• Software*

Publication Types

• Journal Article
• Research Support, Non-U.S. Gov't