SYSTOMONAS -- an integrated database for systems biology analysis of Pseudomonas

• Published in: Nucleic acids research Vol. 35; no. suppl-1; pp. D533 - D537
• Main Authors: Choi, Claudia, Münch, Richard, Leupold, Stefan, Klein, Johannes, Siegel, Inga, Thielen, Bernhard, Benkert, Beatrice, Kucklick, Martin, Schobert, Max, Barthelmes, Jens, Ebeling, Christian, Haddad, Isam, Scheer, Maurice, Grote, Andreas, Hiller, Karsten, Bunk, Boyke, Schreiber, Kerstin, Retter, Ida, Schomburg, Dietmar, Jahn, Dieter
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.01.2007; Oxford Publishing Limited (England)
• Subjects: Bacterial Proteins - classification; Bacterial Proteins - genetics; Bacterial Proteins - physiology; Database Management Systems; Databases, Genetic; Gene Regulatory Networks; Genome, Bacterial; Genomics; Internet; Metabolic Networks and Pathways; Pseudomonas - genetics; Pseudomonas - metabolism; Pseudomonas aeruginosa; Pseudomonas Infections - microbiology; Systems Biology; Systems Integration; User-Computer Interface
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkl823

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.