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About the tools:

Rothamsted Research has been developing a suite of tools called Ondex/QTLNetMiner. Ondex allow users to build genome-scale knowledge networks: networks that integrates custom multi-omics datasets with public databases, including homology, ontologies, QTL databases, as well as biological pathways and the scientific literatures. Comparative genomics and data mining are two powerful approaches to identify key candidate genes in silico. QTLNetMiner allow users to search for trait descriptions over the knowledge networks. The results include lists of genes prioritised based on different types of evidence. All the discoveries can be explored using powerful network analytics and visualisations.

QTL network

QTLNetMiner exploits indirect information and can predict an involvement in a trait based on guilt-by-association principles. This figure shows an excerpt from the gene evidence network, for a user’s query on grain color in wheat. The user provided experimentally-derived 8 differentially expressed genes, which are then found by QTLNetMiner to have an ortholog in the CHS gene from Arabidopsis. Phenotype data as provided by TAIR (green rectangle) and text-mining based relations (blue edge) reveal that CHS loss-of-function mutants show a yellow seed color.



query search

QTLNetMiner lets user to search across various evidence concepts in the knowledge network. The Query Suggester helps user to input alternative synonyms or more specific keywords, grouping them by evidence types: e.g. Gene Ontology Biological Process, Trait Ontology, gene, and protein.


About the programme: 
Members of the programme will have a unique opportunity to preview releases of the software and help steer the project by contributing specific requirements and needs.

Read more about the project here. GenomeWeb article on Genestack and Rothamsted Research collaboration can be found here.


Are you working in applications of genomics to agriculture and want to be a part of this group?


Fill in the form and we will get in touch with you once the tools are ready for testing.


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