SubtiWiki relaunched: a brand-new foundation and novel features

As more and more data from microbiological research is amassed, keeping up to date with the newest findings can be difficult. For this reason, model organism databases attempt to bundle and organize all relevant information on a certain organism, enabling scientists to develop new research hypotheses. We have created SubtiWiki, the most popular freely available database for the model bacterium Bacillus subtilis (1). It holds a wealth of up-to-date curated information as well as datasets from relevant publications. In addition, it features many interactive displays to explore the presented data in an intuitive manner. But as demands on the platform increase, we decided to give SubtiWiki a new foundation, building upon already established web frameworks. This will serve as the basis for a range of additions to the database and its web interface. For instance, we upgraded our Genome Browser by integrating an interactive implementation of the FlaGs tool (2, see figure). It allows users to compare gene neighborhoods among selected representative bacteria, as the analysis of gene order conservation can provide important first hints about the role of a gene. Another extension is the introduction of dedicated pages for metabolites and their integration into the Interaction Browser (see figure). With this, we hope to give a more complete picture of the inner workings of B. subtilis. Yet another update is the implementation of a proper API (Application Programming Interface), which enables programmatic access to SubtiWiki's data for bioinformatics purposes.

We are confident these additions will make SubtiWiki even more useful for the Bacillus research community. In addition, we believe that the structure of our database and web application could serve as a blueprint for future databases dedicated to other microorganisms.

(1) Pedreira, T. et al. (2022) Nucleic Acids Res. 50: D875–D882

(2) Saha, C.K. et al. (2021) Bioinformatics 9: 1312-1314