Connecting parts with processes: SubtiWiki and SubtiPathways integrate gene and pathway annotation for Bacillus subtilis

• Published in: Microbiology (Society for General Microbiology) Vol. 156; no. 3; pp. 849 - 859
• Main Authors: Lammers, Christoph R, Florez, Lope A, Schmeisky, Arne G, Roppel, Sebastian F, Mader, Ulrike, Hamoen, Leendert, Stulke, Jorg
• Format: Journal Article
• Language: English
• Published: Reading Soc General Microbiol 01.03.2010; Society for General Microbiology
• Subjects: Bacillus subtilis - genetics; Bacteriology; Biological and medical sciences; Database Management Systems; Databases, Genetic; Fundamental and applied biological sciences. Psychology; Genes, Bacterial; Microbiology; Miscellaneous; Software; User-Computer Interface; Bacteria; Bacillales; Gene; Bacillaceae; Bacillus subtilis
• ISSN: 1350-0872; 1465-2080
• DOI: 10.1099/mic.0.035790-0

1 Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Germany 2 Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt-Universität Greifswald, Germany 3 Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK Bacillus subtilis is the model organism for a large group of Gram-positive bacteria, the Firmicutes. Several online databases have been established over time to manage its genetic and metabolic information, but they differ greatly in their rate of update and their focus on B. subtilis . Therefore, a European systems biology consortium called for an integrated solution that empowers its users to enrich online content. To meet this goal we created Subti Wiki and Subti Pathways, two complementary online tools for gene and pathway information on B. subtilis 168. Subti Wiki ( http://subtiwiki.uni-goettingen.de/ ) is a scientific wiki for all genes of B. subtilis and their protein or RNA products. Each gene page contains a summary of the most important information; sections on the gene, its product and expression; sections concerning biological materials and laboratories; and a list of references. Subti Wiki has been seeded with key content and can be extended by any researcher after a simple registration, thus keeping it always up to date. As a complement, Subti Pathways ( http://subtipathways.uni-goettingen.de/ ) is an online tool for navigation of the metabolism of B. subtilis and its regulation. Each Subti Pathways diagram presents a metabolic pathway with its participating enzymes, together with the regulatory mechanisms that act on their expression and activity, in an intuitive interface that is based on Google Maps. Together, Subti Wiki and Subti Pathways provide an integrated view of the processes that make up B. subtilis and its components, making it the most comprehensive web resource for B. subtilis researchers. Correspondence Jörg Stülke jstuelk{at}gwdg.de These authors contributed equally to this work.