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Nucleic Acids Research 2007 35(Database issue):D533-D537; doi:10.1093/nar/gkl823
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Nucleic Acids Research, 2007, Vol. 35, Database issue D533-D537
© 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.

Articles

SYSTOMONAS — an integrated database for systems biology analysis of Pseudomonas

Claudia Choi1, Richard Münch1, Stefan Leupold1, Johannes Klein1, Inga Siegel1, Bernhard Thielen2, Beatrice Benkert1, Martin Kucklick1, Max Schobert1, Jens Barthelmes2, Christian Ebeling2, Isam Haddad1, Maurice Scheer1,4, Andreas Grote1,3, Karsten Hiller1, Boyke Bunk1, Kerstin Schreiber1, Ida Retter1, Dietmar Schomburg2 and Dieter Jahn1,*

1 Institut für Mikrobiologie, Technische Universität Braunschweig Spielmannstraße 7, D-38106 Braunschweig, Germany 2 Institut für Biochemie, Universität zu Köln Zülpicher Straße 47, D-50674 Köln, Germany 3 Institut für Bioverfahrenstechnik, Technische Universität Braunschweig Gaußstraße 17, D-38106 Braunschweig, Germany 4 Fachbereich Informatik, Fachhochschule Wolfenbüttel Am Exer 2, D-38302 Wolfenbüttel, Germany

*To whom correspondence should be addressed. Tel: +49 531 391 5801; Fax: +49 531 391 5854; Email: d.jahn{at}tu-bs.de

Received August 11, 2006. Revised October 5, 2006. Accepted October 5, 2006.

To provide an integrated bioinformatics platform for a systems biology approach to the biology of pseudomonads in infection and biotechnology the database SYSTOMONAS (SYSTems biology of pseudOMONAS) was established. Besides our own experimental metabolome, proteome and transcriptome data, various additional predictions of cellular processes, such as gene-regulatory networks were stored. Reconstruction of metabolic networks in SYSTOMONAS was achieved via comparative genomics. Broad data integration is realized using SOAP interfaces for the well established databases BRENDA, KEGG and PRODORIC. Several tools for the analysis of stored data and for the visualization of the corresponding results are provided, enabling a quick understanding of metabolic pathways, genomic arrangements or promoter structures of interest. The focus of SYSTOMONAS is on pseudomonads and in particular Pseudomonas aeruginosa, an opportunistic human pathogen. With this database we would like to encourage the Pseudomonas community to elucidate cellular processes of interest using an integrated systems biology strategy. The database is accessible at http://www.systomonas.de.


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