Award details

Ondex

Reference	BB/F006012/1
Principal Investigator / Supervisor	Professor Robert Stevens
Co-Investigators / Co-Supervisors	Professor Sophia Ananiadou, Professor Carole Goble, Professor Pedro Mendes
Institution	The University of Manchester
Department	Computer Science
Funding type	Research
Value (£)	953,782
Status	Completed
Type	Research Grant
Start date	01/06/2008
End date	30/11/2011
Duration	42 months

Abstract

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).

Summary

See lead application Rothamstead

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	Systems Approaches to Biological Research (SABR) [2007]
Funding Scheme	X – not Funded via a specific Funding Scheme

Associated awards:

BB/F006039/1 From data to knowledge / the ONDEX System for integrating Life Sciences data sources

BB/F006063/1 From data to knowledge / the ONDEX System for integrating Life Sciences data sources

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