BacillOndex

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

• information about basic biological parts (such as CDSs, promoters, operators, terminators, RBS and spacer sequences)
• classification of biological parts based on interactions of gene products and annotations (e.g. GO terms)
• construction and annotation of computational models composed of biological parts

Download

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.

Publications

• DOI BibTeX
  G. Misirli, A. Wipat, J. Mullen, K. James, M. Pocock, W. Smith, N. Allenby, J. Hallinan
  BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology
  in Journal of Integrative Bioinformatics, 10(2):224, 2013

  @ARTICLE{Misirli2013,
    title = {BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology},
    author = {Misirli, G. and Wipat, A. and Mullen, J. and James, K. and Pocock, M. and Smith, W. and Allenby, N. and Hallinan, J.},
    year = 2013,
    doi = {10.2390/biecoll-jib-2013-224},
    journal = {Journal of Integrative Bioinformatics},
    volume = {10},
    number = {2},
    pages = {224}
  }