BacillOndex is an integrated knowledge database for Bacillus subtilis. It combines genome annotations with data about genetic regulatory networks, functional protein-protein interactions, metabolic pathways and microarray experiments. It is represented as a graph with biological concepts as nodes and relationships between them as edges. The database can be visualised and analysed using Ondex, a graph-based data analysis tool.

BacillOndex includes many different types of biological concepts: coding sequence (CDS), protein, transcription factor, operon, operator, promoter, terminator, RNA, enzyme, enzyme classification, reaction, pathway, compound, COG class, COG class category, cellular component, molecular function, biological process, KEGG orthologs enzyme, KEGG orthologs gene, protein complex, KEGG orthologs protein, feed-forward loop, microarray experiment, ribosome binding site (RBS) and spacer sequence.
In total, the database contains 33,043 different concepts and 94,774 relationships.

Synthetic Biology applications


Download BacillOndex: bacill_ondex.xml.gz [5 MiB]
The archive contains an XML file in Ondex format.

Download VirtualBox image: bacill_ondex_virtual_box.tgz [1.4 GiB]
Virtual machine image with entire BacillOndex system.