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Database Profile

General information

URL: http://subtiwiki.uni-goettingen.de/
Full name: A community resource for the model organism Bacillus subtilis
Description: A database for the model organism Bacillus subtilis that links pathway, interaction and expression information
Year founded: 2009
Last update: 2016-01-04
Version: v2.0
Accessibility:
Manual:
Accessible
Real time : Checking...
Country/Region: Germany
Data type:
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: Georg August University
Address: Grisebachstr. 8, D-37077 Göttingen, Germany
City: Göttingen
Province/State:
Country/Region: Germany
Contact name (PI/Team): Jörg Stülke
Contact email (PI/Helpdesk): jstuelk@gwdg.de

Publications

29788229
SubtiWiki in 2018: from genes and proteins to functional network annotation of the model organism Bacillus subtilis. [PMID: 29788229]
Zhu B, Stülke J.

Living cells are made up of individual parts, i.e. the genome, the proteins, the RNA and lipid molecules as well as the metabolites and ions. However, life depends on the functional interaction among these components which is often organized in networks. Here, we present the recent development of SubtiWiki, the integrated database for the model bacterium Bacillus subtilis (http://subtiwiki.uni-goettingen.de/). SubtiWiki is based on a relational database and provides access to published information about the genes and proteins of B. subtilis and about metabolic and regulatory pathways. We have included a network visualization tool that can be used to visualize regulatory as well as protein-protein interaction networks. The resulting interactive graphical presentations allow the user to detect novel associations and thus to develop novel hypotheses that can then be tested experimentally. To facilitate the mobile use of SubtiWiki, we provide enhanced versions of the SubtiWiki App that are available for iOS and Android devices. Importantly, the App allows to link private notes and pictures to the gene/protein pages that can be synchronized on multiple devices. SubtiWiki has become one of the most complete resources of knowledge on a living organism.

Nucleic Acids Res. 2018:46(D1) | 64 Citations (from Europe PMC, 2021-06-19)
26433225
SubtiWiki 2.0--an integrated database for the model organism Bacillus subtilis. [PMID: 26433225]
Michna RH, Zhu B, Mäder U, Stülke J.

To understand living cells, we need knowledge of each of their parts as well as about the interactions of these parts. To gain rapid and comprehensive access to this information, annotation databases are required. Here, we present SubtiWiki 2.0, the integrated database for the model bacterium Bacillus subtilis (http://subtiwiki.uni-goettingen.de/). SubtiWiki provides text-based access to published information about the genes and proteins of B. subtilis as well as presentations of metabolic and regulatory pathways. Moreover, manually curated protein-protein interactions diagrams are linked to the protein pages. Finally, expression data are shown with respect to gene expression under 104 different conditions as well as absolute protein quantification for cytoplasmic proteins. To facilitate the mobile use of SubtiWiki, we have now expanded it by Apps that are available for iOS and Android devices. Importantly, the App allows to link private notes and pictures to the gene/protein pages. Today, SubtiWiki has become one of the most complete collections of knowledge on a living organism in one single resource. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nucleic Acids Res. 2016:44(D1) | 38 Citations (from Europe PMC, 2021-06-19)
24178028
SubtiWiki-a database for the model organism Bacillus subtilis that links pathway, interaction and expression information. [PMID: 24178028]
Michna RH, Commichau FM, Tödter D, Zschiedrich CP, Stülke J.

Genome annotation and access to information from large-scale experimental approaches at the genome level are essential to improve our understanding of living cells and organisms. This is even more the case for model organisms that are the basis to study pathogens and technologically important species. We have generated SubtiWiki, a database for the Gram-positive model bacterium Bacillus subtilis (http://subtiwiki.uni-goettingen.de/). In addition to the established companion modules of SubtiWiki, SubtiPathways and SubtInteract, we have now created SubtiExpress, a third module, to visualize genome scale transcription data that are of unprecedented quality and density. Today, SubtiWiki is one of the most complete collections of knowledge on a living organism in one single resource.

Nucleic Acids Res. 2014:42(Database issue) | 40 Citations (from Europe PMC, 2021-06-19)
22096228
SubtiWiki--a comprehensive community resource for the model organism Bacillus subtilis. [PMID: 22096228]
Mäder U, Schmeisky AG, Flórez LA, Stülke J.

In the post-genomic era, most components of a cell are known and they can be quantified by large-scale functional genomics approaches. However, genome annotation is the bottleneck that hampers our understanding of living cells and organisms. Up-to-date functional annotation is of special importance for model organisms that provide a frame of reference for studies with other relevant organisms. We have generated a Wiki-type database for the Gram-positive model bacterium Bacillus subtilis, SubtiWiki (http://subtiwiki.uni-goettingen.de/). This Wiki is centered around the individual genes and gene products of B. subtilis and provides information on each aspect of gene function and expression as well as protein activity and its control. SubtiWiki is accompanied by two companion databases SubtiPathways and SubtInteract that provide graphical representations of B. subtilis metabolism and its regulation and of protein-protein interactions, respectively. The diagrams of both databases are easily navigatable using the popular Google maps API, and they are extensively linked with the SubtiWiki gene pages. Moreover, each gene/gene product was assigned to one or more functional categories and transcription factor regulons. Pages for the specific categories and regulons provide a rapid overview of functionally related genes/proteins. Today, SubtiWiki can be regarded as one of the most complete inventories of knowledge on a living organism in one single resource.

Nucleic Acids Res. 2012:40(Database issue) | 43 Citations (from Europe PMC, 2021-06-19)
19959575
Connecting parts with processes: SubtiWiki and SubtiPathways integrate gene and pathway annotation for Bacillus subtilis. [PMID: 19959575]
Lammers CR, Flórez LA, Schmeisky AG, Roppel SF, Mäder U, Hamoen L, Stülke J.

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.

Microbiology. 2010:156(Pt 3) | 25 Citations (from Europe PMC, 2021-06-19)
20157485
A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki. [PMID: 20157485]
Flórez LA, Roppel SF, Schmeisky AG, Lammers CR, Stülke J.

Bacillus subtilis is the model organism for Gram-positive bacteria, with a large amount of publications on all aspects of its biology. To facilitate genome annotation and the collection of comprehensive information on B. subtilis, we created SubtiWiki as a community-oriented annotation tool for information retrieval and continuous maintenance. The wiki is focused on the needs and requirements of scientists doing experimental work. This has implications for the design of the interface and for the layout of the individual pages. The pages can be accessed primarily by the gene designations. All pages have a similar flexible structure and provide links to related gene pages in SubtiWiki or to information in the World Wide Web. Each page gives comprehensive information on the gene, the encoded protein or RNA as well as information related to the current investigation of the gene/protein. The wiki has been seeded with information from key publications and from the most relevant general and B. subtilis-specific databases. We think that SubtiWiki might serve as an example for other scientific wikis that are devoted to the genes and proteins of one organism.Database URL: The wiki can be accessed at http://subtiwiki.uni-goettingen.de/

Database (Oxford). 2009:2009() | 16 Citations (from Europe PMC, 2021-06-19)

Ranking

All databases:
460/5061 (90.931%)
Expression:
63/924 (93.29%)
Interaction:
72/771 (90.791%)
460
Total Rank
226
Citations
18.833
z-index

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Word cloud

Record metadata

Created on: 2015-06-20
Curated by:
Amjad Ali [2019-10-26]
Zhang Zhang [2016-05-08]
Lin Xia [2016-03-28]
Mengwei Li [2016-02-19]
lin liu [2016-02-02]
lin liu [2016-01-17]
Lin Xia [2015-06-26]