The development of an integrated database of the model organism Bacillus subtilis

by Raphael Michna
Doctoral thesis
Date of Examination:2016-01-13
Date of issue:2016-01-25
Advisor:Prof. Dr. Jörg Stülke
Referee:Prof. Dr. Jörg Stülke
Referee:Prof. Dr. Burkhard Morgenstern
Referee:Dr. Fabian Moritz Commichau
Persistent Address: http://dx.doi.org/10.53846/goediss-5469

 

 

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Abstract

English

In the era of “Omics” approaches, the available data is exponentially increasing and new methods must be invented to handle this data. For this purpose, databases store, maintain and provide the data, and algorithms provide the possibility for further analyzing, clustering or organizing the datasets. Bacillus subtilis is a well-studied model bacterium which is a prerequisite for further scientific research. SubtiWiki is a database storing the annotated information on genes of B. subtilis. This database is curated by the Bacillus community which keeps it up to date. Unfortunately, the mediawiki engine provides the information in raw text and the properties of a gene are not directly usable in bioinformatic approaches. The main properties of the gene are hidden in raw text of the SubtiWiki pages. Here we altered the layout of the database, extracted the information from the wiki pages and created a completely new website. In the beginning, the relevant information was filtered out from the wiki pages via text mining. In parallel, the extracted properties of a gene were organized and then inserted in the new database structure. The content of the applications (SubtInteract, SubtiPathways, SubtiExpress) was adapted to the new database layout to extend the information of the gene. Finally, the web sites obtained a new design. As a result, SubtiWiki is not a classical “Wiki” anymore but the idea of fast editing and community curation remains. Thus, this database moved to a classical database structure which can be used for bioinformatic approaches and it simplifies maintenance of the data. SubtiWiki becomes a powerful database covering genes, pathways, expression-levels and protein-protein interactions of B. subtilis but the analysis and comparison of the properties and networks recently began. The newly constructed database and the new web performance facilitate new insights in B. subtilis. Moreover, the tools for the analysis and especially visualization were adapted and improved to fit to the new database layout. The tools and the data are now easily accessible for the user and SubtiWiki is prepared to integrate high-throughput data.
Keywords: Database; Bacillus subtilis; web application
 
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