Connecting parts with processes: SubtiWiki and SubtiPathways integrate gene and pathway annotation for Bacillus subtilis.
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 SubtiWiki and SubtiPathways, two complementary online tools for gene and pathway information on B. subtilis 168. SubtiWiki (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. SubtiWiki 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, SubtiPathways (http://subtipathways.uni-goettingen.de/) is an online tool for navigation of the metabolism of B. subtilis and its regulation. Each SubtiPathways 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, SubtiWiki and SubtiPathways 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.
Lammers
Christoph R
CR
Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Germany.
Flórez
Lope A
LA
Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Germany.
Schmeisky
Arne G
AG
Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Germany.
Roppel
Sebastian F
SF
Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Germany.
Mäder
Ulrike
U
Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt-Universität Greifswald, Germany.
Hamoen
Leendert
L
Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK.
Stülke
Jörg
J
Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Germany.
D001412:Bacillus subtilis / Q000235:genetics*; D003628:Database Management Systems; D030541:Databases, Genetic; D005798:Genes, Bacterial; D012984:Software; D014584:User-Computer Interface