1887

Abstract

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 . 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 Wiki and Pathways, two complementary online tools for gene and pathway information on 168. Wiki (http://subtiwiki.uni-goettingen.de/) is a scientific wiki for all genes of 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. 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, Pathways (http://subtipathways.uni-goettingen.de/) is an online tool for navigation of the metabolism of and its regulation. Each 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, Wiki and Pathways provide an integrated view of the processes that make up and its components, making it the most comprehensive web resource for researchers.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.035790-0
2010-03-01
2019-10-16
Loading full text...

Full text loading...

/deliver/fulltext/micro/156/3/849.html?itemId=/content/journal/micro/10.1099/mic.0.035790-0&mimeType=html&fmt=ahah

References

  1. Barbe, V., Cruveiller, S., Kunst, F., Lenoble, P., Meurice,G., Sekowska, A., Vallenet, D., Wang, T., Moszer, I. & other authors ( 2009; ). From a consortium sequence to a unified sequence:the Bacillus subtilis 168 reference genome a decade later. Microbiology 155, 1758–1775.[CrossRef]
    [Google Scholar]
  2. Berman, H., Henrick, K., Nakamura, H. & Markley, J. L. ( 2007; ). The worldwide Protein Data Bank (wwPDB):ensuring a single, uniform archive of PDB data. Nucleic Acids Res 35, D301–D303.[CrossRef]
    [Google Scholar]
  3. Flórez, L. A., Roppel, S. F., Schmeisky, A. G., Lammers,C. R. & Stülke, J. ( 2009; ). A community-curatedconsensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki. Database
    [Google Scholar]
  4. Goelzer, A., Bekkal-Brikci, F., Martin-Verstraete, I., Noirot,P., Bessières, P., Aymerich, S. & Fromion, V. ( 2008; ). Reconstruction and analysis of the genetic and metabolic regulatorynetworks of the central metabolism of Bacillus subtilis. BMC Syst Biol 2, 20 [CrossRef]
    [Google Scholar]
  5. Goll, J., Rajagopala, S. V., Shiau, S. C., Wu, H., Lamb, B.T. & Uetz, P. ( 2008; ). MPIDB: the microbial proteininteraction database. Bioinformatics 24, 1743–1744.[CrossRef]
    [Google Scholar]
  6. Grote, A., Klein, J., Retter, I., Haddad, I., Behling, S., Bunk,B., Biegler, I., Yarmolinetz, S., Jahn, D. & Münch, R. ( 2009; ). PRODORIC (release 2009): a database and tool platformfor the analysis of gene regulation in prokaryotes. Nucleic AcidsRes 37, D61–D65.
    [Google Scholar]
  7. Henry, C. S., Zinner, J. F., Cohoon, M. P. & Stevens, R.L. ( 2009; ). iBsu1103: a new genome-scale metabolicmodel of Bacillus subtilis based on SEED annotations. Genome Biol 10, R69 [CrossRef]
    [Google Scholar]
  8. Hodis, E., Prilusky, J., Martz, E., Silman, I., Moult, J. &Sussman, J. L. ( 2008; ). Proteopedia –a scientific “wiki” bridging the rift between three-dimensionalstructure and function of biomacromolecules. Genome Biol 9, R121 [CrossRef]
    [Google Scholar]
  9. Hoffmann, R. ( 2008; ). A wiki for thelife sciences where authorship matters. Nat Genet 40, 1047–1051.[CrossRef]
    [Google Scholar]
  10. Hu, J. C., Aramayo, R., Bolser, D., Conway, T., Elsik, C. G.,Gribskov, M., Kelder, T., Kihara, D., Knight, T. F. & other authors ( 2008; ). The emerging world of wikis. Science 320, 1289–1290.
    [Google Scholar]
  11. Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M.,Itoh, M., Katayama, T., Kawashima, S., Okuda, S. & other authors ( 2008; ). KEGG for linking genomes to life and the environment. Nucleic Acids Res 36, D480–D484.
    [Google Scholar]
  12. Karp, P. D., Ouzounis, C. A., Moore-Kochlacs, C., Goldovsky,L., Kaipa, P., Ahrén, D., Tsoka, S., Darzentas, N., Kunin, V. &López-Bigas, N. ( 2005; ). Expansion of the BioCyccollection of pathway/genome databases to 160. Nucleic AcidsRes 33, 6083–6089.
    [Google Scholar]
  13. Kitano, H., Funahashi, A., Matsuoka, Y. & Oda, K. ( 2005; ). Using process diagrams for the graphical representationof biological networks. Nat Biotechnol 23, 961–966.[CrossRef]
    [Google Scholar]
  14. Kulikova, T., Akhtar, R., Aldebert, P., Althorpe, N., Andersson,M., Baldwin, A., Bates, K., Bhattacharyya, S., Bower, L. & other authors ( 2007; ). EMBL Nucleotide database in 2006. Nucleic Acids Res 35, D16–D20.[CrossRef]
    [Google Scholar]
  15. Kunst, F., Ogasawara, N., Moszer, I., Albertini, A., Alloni,G., Azevedo, V., Bertero, M., Bessieres, P., Bolotin, A. & other authors ( 1997; ). The complete genome sequence of the Gram-positivebacterium Bacillus subtilis. Nature 390, 249–256.[CrossRef]
    [Google Scholar]
  16. Lechat, P., Hummel, L., Rousseau, S. & Moszer, I. ( 2008; ). GenoList: an integrated environment for comparativeanalysis of microbial genomes. Nucleic Acids Res 36, D469–D474.
    [Google Scholar]
  17. Le Novère, N., Hucka, M., Mi, H., Moodie, S., Schreiber,F., Sorokin, A., Demir, E., Wegner, K., Aladjem, M. I. & other authors ( 2009; ). The Systems Biology Graphical Notation. Nat Biotechnol 27, 735–741.[CrossRef]
    [Google Scholar]
  18. Mons, B., Ashburner, M., Chichester, C., van Mulligen, E., Weeber,M., den Dunnen, J., van Ommen, G. J., Musen, M., Cockerill, M. & otherauthors ( 2008; ). Calling on a million minds for communityannotation in WikiProteins. Genome Biol 9, R89 [CrossRef]
    [Google Scholar]
  19. Moszer, I., Glaser, P. & Danchin, A. ( 1995; ). SubtiList: a relational database for the Bacillus subtilis genome. Microbiology 141, 261–268.[CrossRef]
    [Google Scholar]
  20. Moszer, I., Jones, L. M., Moreira, S., Fabry, C. & Danchin,A. ( 2002; ). SubtiList: the reference database for the Bacillus subtilis genome. Nucleic Acids Res 30, 62–65.[CrossRef]
    [Google Scholar]
  21. Oh, Y. K., Palsson, B. O., Park, S. M., Schilling, C. H. &Mahadevan, R. ( 2007; ). Genome-scale reconstructionof metabolic network in Bacillus subtilis based on high-throughputphenotyping and gene essentiality data. J Biol Chem 282, 28791–28799.[CrossRef]
    [Google Scholar]
  22. Pico, A. R., Kelder, T., van Iersel, M. P., Hanspers, K., Conklin,B. R. & Evelo, C. ( 2008; ). WikiPathways: pathwayediting for the people. PLoS Biol 6, e184 [CrossRef]
    [Google Scholar]
  23. Sierro, N., Makita, Y., de Hoon, M. & Nakai, K. ( 2008; ). DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res 36, D93–D96.[CrossRef]
    [Google Scholar]
  24. Stokes, T. H., Torrance, J. T., Li, H. & Wang, M. D. ( 2008; ). ArrayWiki: an enabling technology for sharing publicmicroarray data repositories and meta-analyses. BMC Bioinformatics 9, S18
    [Google Scholar]
  25. Uniprot Consortium ( 2009; ). The UniversalProtein Resource (UniProt) 2009. Nucleic Acids Res 37, D169–D174.[CrossRef]
    [Google Scholar]
  26. von Ahn, L., Maurer, B., McMillen, C., Abraham, D. & Blum,M. ( 2008; ). reCAPTCHA: human-based character recognitionvia Web security measures. Science 321, 1465–1468.[CrossRef]
    [Google Scholar]
  27. Waldrop, M. ( 2008; ). Big data: Wikiomics. Nature 455, 22–25.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.035790-0
Loading
/content/journal/micro/10.1099/mic.0.035790-0
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error