BacillOndex

Project Description

BacillOndex is an integrated knowledge base for Bacillus subtilis. The knowledge base combines genome annotations with data about genetic regulatory networks, biochemical reactions, microarray experiments and protein-protein interactions. BacillOndex is implemented as a semantically-enriched network in which nodes represent biological concepts such as genes and gene products, and the edges represent the relationships between these concepts. The network can be visualised and analysed using Ondex, a graph based data analysis tool.

Types of concepts included in the network: 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 (Shim). The knowledge base includes 33,043 different concepts and 94,774 relationships between them. The figure below is the data model for the integrated dataset. The diagram shows the concept types and the major relationships for visual clarity. Shapes and lines represent the types of concepts and relationships respectively.

BacillOndex Model

Synthetic Biology

This knowledge base is suitable to extract information about basic biological parts, such as CDSs, promoters, operators, terminators, RBS, and spacer sequences, for synthetic biology. Furthermore, information about the interactions of gene products and annotations, such as those that are specified by GO terms, can be used to classify biological parts in order to rationally design synthetic genetic circuits. This information is also used to construct and annotate computational models of these parts, when combined with biochemical parameters.

Example: mntR CDS2

The details of the mntR CDS concept from the network are shown in the figure below. The nucleotide sequence, gene expression values and the annotations are the stored as attributes of the CDS concept.
BacillOndex mntR Gene

Example: ccdA promoter

Attributes for the ccdA promoter concept includes the nucleotide sequence, start and end positions on the chromosome and the Pubmed ID.
BacillOndex ccdA Promoter

Example: Spo0A regulation

An example network of Spo0A and the its regulated genes are shown in the figure.
Example Network 1

Spo0A and KinA are two central concepts in the example network below. The relationships indicate how Spo0A is phosphorylated by kinases in a multi-component phosphorelay.
Spo0A and KinA Network

Publications

  1. Misirli G, Hallinan JS, Pocock M, Cockell SJ, Weile J, Wipat A. BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology. Newcastle upon Tyne: School of Computing Science, University of Newcastle upon Tyne, 2011. School of Computing Science Technical Report Series 1237.
  2. Misirli, G., Hallinan, J. S., Pocock, M., Cockell, S. J., Weile, J. and Wipat, A. (2011). BacillOndex: An integrated data resource for systems and synthetic biology. Poster at 6th International Conference on Gram-positive Microorganisms. Montecatini Terme, Tuscany, Italy.
  3. Misirli, G., Hallinan, J., Pocock, M., Cockell, S. J., Weile, J. and Wipat, A. (2011). BacillOndex: An integrated data resource for systems and synthetic biology. Poster at SB5.0 The Fifth International Meeting on Synthetic Biology. Stanford University, Stanford, California USA.

Download

There are two ways in which the BacillOndex dataset may be viewed and analysed. The user can manually download and install both Ondex and the dataset file, as described here. Alternatively, the entire BacillOndex system can be downloaded as a Virtual Machine. To view the BacillOndex dataset, install Ondex and load the dataset into Ondex as explained below.

  1. Install Ondex
    • Download and install Ondex's ICSB 2010 release . The dataset was tested with Ondex's ICSB 2010 release.
    • If you are using the Windows installer, make sure to click to the Ondex Integrator checkbox to install the integrator.
    • For more information see the Installation section in the Ondex tutorial.
  2. Download the BacillOndex dataset.
  3. Load the dataset into Ondex
    • Launch Ondex (Use the start menu in Windows or runme.sh from the Ondex directory in Linux), click on File -> Open in the menu bar, and select the downloaded dataset.

BacillOndex Files