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.
BarbeV.,
CruveillerS.,
KunstF.,
LenobleP.,
MeuriceG.,
SekowskaA.,
VallenetD.,
WangT.,
MoszerI.other authors2009; From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later. Microbiology 155:1758–1775
BermanH.,
HenrickK.,
NakamuraH.,
MarkleyJ. L.2007; The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res 35:D301–D303
FlórezL. A.,
RoppelS. F.,
SchmeiskyA. G.,
LammersC. R.,
StülkeJ.2009; A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki. Database:
GoelzerA.,
Bekkal-BrikciF.,
Martin-VerstraeteI.,
NoirotP.,
BessièresP.,
AymerichS.,
FromionV.2008; Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis. BMC Syst Biol 2:20
GroteA.,
KleinJ.,
RetterI.,
HaddadI.,
BehlingS.,
BunkB.,
BieglerI.,
YarmolinetzS.,
JahnD.,
MünchR.2009; PRODORIC (release 2009): a database and tool platform for the analysis of gene regulation in prokaryotes. Nucleic Acids Res 37:D61–D65
HenryC. S.,
ZinnerJ. F.,
CohoonM. P.,
StevensR. L.2009; iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations. Genome Biol 10:R69
HodisE.,
PriluskyJ.,
MartzE.,
SilmanI.,
MoultJ.,
SussmanJ. L.2008; Proteopedia – a scientific “wiki” bridging the rift between three-dimensional structure and function of biomacromolecules. Genome Biol 9:R121
KanehisaM.,
ArakiM.,
GotoS.,
HattoriM.,
HirakawaM.,
ItohM.,
KatayamaT.,
KawashimaS.,
OkudaS.other authors2008; KEGG for linking genomes to life and the environment. Nucleic Acids Res 36:D480–D484
KarpP. D.,
OuzounisC. A.,
Moore-KochlacsC.,
GoldovskyL.,
KaipaP.,
AhrénD.,
TsokaS.,
DarzentasN.,
KuninV.,
López-BigasN.2005; Expansion of the BioCyc collection of pathway/genome databases to 160. Nucleic Acids Res 33:6083–6089
KitanoH.,
FunahashiA.,
MatsuokaY.,
OdaK.2005; Using process diagrams for the graphical representation of biological networks. Nat Biotechnol 23:961–966
LechatP.,
HummelL.,
RousseauS.,
MoszerI.2008; GenoList: an integrated environment for comparative analysis of microbial genomes. Nucleic Acids Res 36:D469–D474
Le NovèreN.,
HuckaM.,
MiH.,
MoodieS.,
SchreiberF.,
SorokinA.,
DemirE.,
WegnerK.,
AladjemM. I. & other authors (2009. The Systems Biology Graphical Notation. Nat Biotechnol 27:735–741
MonsB.,
AshburnerM.,
ChichesterC.,
van MulligenE.,
WeeberM.,
den DunnenJ.,
van OmmenG. J.,
MusenM.,
CockerillM.other authors2008; Calling on a million minds for community annotation in WikiProteins. Genome Biol 9:R89
MoszerI.,
JonesL. M.,
MoreiraS.,
FabryC.,
DanchinA.2002; SubtiList: the reference database for the Bacillus subtilis genome. Nucleic Acids Res 30:62–65
OhY. K.,
PalssonB. O.,
ParkS. M.,
SchillingC. H.,
MahadevanR.2007; Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data. J Biol Chem 282:28791–28799
SierroN.,
MakitaY.,
de HoonM.,
NakaiK.2008; DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res 36:D93–D96
StokesT. H.,
TorranceJ. T.,
LiH.,
WangM. D.2008; ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses. BMC Bioinformatics 9:S18