Award details

From data to knowledge: the ONDEX System for integrating life sciences data resources

Reference	BBS/E/C/00004918
Principal Investigator / Supervisor	Professor Christopher Rawlings
Co-Investigators / Co-Supervisors
Institution	Rothamsted Research
Department	Rothamsted Research Department
Funding type	Research
Value (£)	303,459
Status	Completed
Type	Institute Project
Start date	01/04/2008
End date	30/11/2011
Duration	44 months

Abstract

The aim of this project is to develop an extensible data integration system for supporting systems biology research. The project will extend the ONDEX data integration platform (http://ondex.sf.net) and support four demonstrator projects at three Centres for Integrated Systems Biology (CISB). The demonstrator projects represent a range of general data integration problems in systems biology and will exercise and validate new features through direct interaction with end-users. The three core demonstrator projects will: identify new genetic and molecular targets to improve bioenergy crops (Rothamsted); integrate, and validate different yeast metabolome models (Manchester, MCISB) and support studies of telomere function relating to ageing research in yeast (Newcastle, CISBAN). A fourth demonstrator project at the CSBE (Edinburgh) will study signal transduction processes controlling circadian rhythms in Arabidopsis thaliana. The ONDEX system has been developed as a generic solution to semantic integration of life science data using a warehousing approach based on a generic graph data structure. Integration is achieved by a set of mapping functions that populate the data graph with additional equivalence relationships. The parsing and mapping features implemented in ONDEX enable a wide range of data to be integrated including sequence databases, microarray information, transcription factor databases (e.g. Transfac), biological pathway databases (e.g. KEGG), gene function and biological ontologies (e.g. from the OBO foundry). In addition there are mapping functions that implement text mining features. During this project, new features and improvements will be made to increase the range of system biology projects that can be supported. An important part of the project will be to provide outreach and support to new users and a key objective will be to engage with a wider range of BBSRC-funded systems biology projects.

Summary

unavailable

Committee	Closed Committee - Engineering & Biological Systems (EBS)
Research Topics	Bioenergy, Industrial Biotechnology, Systems Biology, Technology and Methods Development
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	X – not Funded via a specific Funding Scheme

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