Ondex

Project Description

The Ondex data integration platform enables data from diverse biological data sets to be linked, integrated and visualised through graph analysis techniques. Ondex uses a rich and flexible core data structure, which has the ability to bring together information from structured databases and unstructured sources such as biological sequence data and free text. Ondex also allows users to visualise and analyse the integrated data.

Ondex is open source project that has been under development for a number of years now. In 2008, the BBSRC provided funding under the SABR initiative to develop Ondex as a resource for the systems biology community. The main partners are Rothamsted Research, The University of Edinburgh, The University of Manchester and Newcastle University.

You can read more about the Ondex project in general, and download the system, on the main Ondex SABR website here.

At Newcastle we have been involved in the development of the Ondex architecture and also have developed a number of applications of Ondex in the systems biology area:

  • The Ondex system has been tailored to the study of the systems biology of ageing in yeast in collaboration with Prof. David Lydall and the CISBAN team.
  • Integrated datasets that allow drug repurposing opportunities have been developed in collaboration with industrial partners such as e-Therapeutics and, more recently, GlaxoSmithKline
  • We have developed a plugin that allows Ondex to interface with the Cytoscape system
  • An Ondex plugin has been developed for the systems level analysis of single nucleotide polymorphisms (SNPs). CatSNP allows the impact of single nucleotide genetic changes to be investigated and their effect on interactions and metabolic/signalling pathways to be investigated
  • We have developed an integrated dataset for the systems biology of Bacillus subtilis called BacillOndex
  • We are using the BacillOndex dataset to inform the design of biological systems to support the synthetic biology of Bacillus subtilis

Funding

The Ondex project is funded by the BBSRC:

  1. BB/F529038/1: Systems approaches to biological research training grant
  2. BB/F006063/1: From data to knowledge / the ONDEX System for integrating Life Sciences data sources