From data to knowledge : the ONDEX System for integrating Life Sciences data sources

Completed

Not Energy Related
Renewable Energy Sources(Bio-Energy, Other bio-energy)

Basic and strategic applied research

BIOLOGICAL AND AGRICULTURAL SCIENCES (Biological Sciences)

Not Cross-cutting

Prof C Rawlings
Computational and Systems Biology
Rothamsted Research

Research Grant

BBSRC

01 April 2008

30 November 2011

44 months

£1,148,119

Pharmaceuticals and Biotechnology

East of England

Systems Approaches to Biological Research (SABR)

Prof C Rawlings, Computational and Systems Biology, Rothamsted Research

Dr A Karp, Agro-Ecology, Rothamsted Research
Dr J Koehler, Rothamsted Research

This grant is linked to BB/F006063/1, BB/F006012/1 and BBS/E/C/00004918 .

The current ONDEX system enables data from diverse biological data set to be linked, integrated and visualised through graph analysis techniques. It uses a semantically rich Core data structure based on graphs, has explicit support for workflow and has the ability to bring together information from structured databases and unstructured sources such as sequence data and free text. Extensions for Systems Biology include: Enhancing the ONDEX Core: - Methods to map data into the core data structures to exploit synteny and sequence similarity for applications needing comparative analysis of genetic and genomic organisation of multiple organisms. -Techniques for probabilistic interpretation of relations allowing uncertainty in the integrated data and in biological relationships to be modelled, combining relations using probabilistic models such as naive Bayesian and Bayesian graphical Gaussian approaches. Exploiting the ONDEX data graph: A graph structure analysis toolkit using, standard and advanced graph analysis algorithms, that traverses the data graph and modules representing common structural and functional components to be identified. Populating the ONDEX model: - Orchestrating data integration and analysis steps in ONDEX applications, using Taverna workflows and services (myGrid), including the running of workflows. Using Taverna will allow ONDEX to retain data on workflow provenance, which can be used to track, verify and validate data. - Enhanced text mining methods to extract and map terms from text in databases and online literature sources to detect synonymy and ambiguity and the identification and extraction biologically relevant relations. Exposing ONDEX to tools: New data access interfaces to allow ONDEX data to be used by third party tools, e.g. within workflows, and data export tools to provide easy access to ONDEX data for users of Cytoscape and for export in standard systems biology model exchange formats (e.g. SBML, BioPAX etc).

30/09/13