Projects
Projects: Projects for Investigator |
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| Reference Number | BB/I023860/1 | |
| Title | QTLNetMiner: Mining Candidate Gene Networks From Genetic Studies of Crops and Animals | |
| Status | Completed | |
| Energy Categories | Not Energy Related 20%; Renewable Energy Sources(Bio-Energy, Applications for heat and electricity) 80%; |
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| Research Types | Basic and strategic applied research 100% | |
| Science and Technology Fields | BIOLOGICAL AND AGRICULTURAL SCIENCES (Biological Sciences) 50%; PHYSICAL SCIENCES AND MATHEMATICS (Computer Science and Informatics) 50%; |
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| UKERC Cross Cutting Characterisation | Not Cross-cutting 100% | |
| Principal Investigator |
Prof C (Chris ) Rawlings No email address given Computational and Systems Biology Rothamsted Research |
|
| Award Type | Research Grant | |
| Funding Source | BBSRC | |
| Start Date | 03 January 2012 | |
| End Date | 02 March 2013 | |
| Duration | 14 months | |
| Total Grant Value | £100,285 | |
| Industrial Sectors | Manufacturing | |
| Region | East of England | |
| Programme | Tools and Resources Development Fund (TRDF) | |
| Investigators | Principal Investigator | Prof C (Chris ) Rawlings , Computational and Systems Biology, Rothamsted Research (100.000%) |
| Web Site | ||
| Objectives | The impact plan for this short sTRDF project focuses on promoting the potential benefits to crop and animal pre-breeding and genetics research through using the tools we are developing to exploit integrated bioinformatics data resources and network analysis methods in the translation of knowledge from model species (e.g. Arabidopsis, Human, Mouse) to a better understanding of complex trait biology. This project will develop advanced prototypes that could be extended for the benefit of other crop and livestock species. We are thus creating a proof of principal for a general approach and platform bioinformatics technology that could be deployed more broadly and with the associated increase in impact. We also consider that the resources being created by QTLNetMiner will be a showcase for how data-intensive biology can be exploited for the benefit of plant and animal science. The impact of the project in the crop science community will be addressed through engagement by the Rothamsted group with the commercial and academic partners in the BBSRC Sustainable Bioenergy Centre consortium. The Poplar knowledge base will be used and tested by the Willow geneticists and breeders at Rothamsted. Any potentially valuable candidate genes identified with the willow genetics team would potentially be evaluated for suitable intellectual property protection by Rothamsted or in partnership with PBL Technology. The Rawlings group is also involved with other crop science communities (wheat and brassica) and during this project we will be participating in stakeholder events (e.g. the WGIN and OREGIN genetic improvement networks) where we will look to demonstrate the potential impact of the QTLNetMiner tools and resources. We will be using the working prototypes developed in this project to engage with the livestock and veterinary research communities. The recent incorporation of the Roslin Institute with the Royal (Dick) School of Veterinary Studies provides excellent opportunitiesto engage with a wider range of animal and veterinary scientists in the private sector. Andy Law will lead this aspect of our impact activities. Roslin scientists have particular sectoral expertise and industry engagement activities, not just with commercial animal breeding companies but with the pharmaceutical sector who use animal models of human diseases in their research programmes. We will work through the Roslin Division of Genetics and Genomics and Business Development Executive to identify where best to focus our outreach activities given the limited resources and duration of this project. Note : Grant BB/I023690/1 is linked to this grant but has not been included in the Register as it is solely concerned with animal species. | |
| Abstract | The Ondex data integration platform uses graph based methods to integrate biological data sources based on concepts of semantic mapping. In a novel development of the Ondex system we will create a client-server application framework based on Web Services and a lightweight Ondex user interface and visualisation framework (QTLNetMiner) that will support biologists mining genetics and genomics data resources for the networks of information and interactions that can be used to select functional candidate genes from QTL studies. We will re-use and substantially adapt components from the Ondex data integration framework developed in a BBSRC SABR project to create integrated knowledge bases constructed from genetics, genome sequence, trait and gene function ontologies, protein family and biochemical pathway and enzyme function information together with Medline abstracts for four sequenced species of agronomic interest. We have selected the tree species Poplar (used as a model for Willow as a bioenergy crop) and three livestock species (Pig, Cow and Chicken) to demonstrate that our data integration methods and software architecture can be adapted to completely new areas of biology in a cost effective way. Our objective will be to create four separate novel biologist-friendly web resources as working prototypes that will enable users to search the crop and livestock genetics datasets using searches based on visualisation of QTL data using a third-party application (GViewer), keyword and regular expression and through inference over the network of relationships in each species-specific knowledge base. The subnetworks retrieved will be displayed using a new and extended web-enabled version of the Ondex client application and this will allow the user to perform visualisation and interactive analysis of the relevant subsection of the knowledgebase to support network-based evaluation of the sets of positional candidate derived from genetics studies. | |
| Publications | (none) |
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| Final Report | (none) |
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| Added to Database | 22/11/13 | |
