MINING THE MOTHER LODE
Search tool uncovering new findings amongst the mountains of data
The avalanche of 21st Century genomic and post-genomic data had led to something of a new phenomenon for biologists: ‘too much information’.
However, a new study in the Plant Biotechnology Journal outlines a Rothamsted developed software package that is helping researchers manage the overload.
KnetMiner is described by its creators as the first ‘gene discovery platform’ for the biological sciences, unearthing previously unknown links between genes, gene networks and traits by searching across species and the boundaries between academic disciplines.
“KnetMiner makes biological search more integrated, intuitive and intelligent, enabling a better way to discover and share new insights,” says project leader Dr Keywan Hassani-Pak.
“The generation of new ideas and scientific hypotheses is often the result of interpreting new data in the context of extensive literature and database searches, but, with the growing wealth of public and private knowledge, the process of searching through all this data to generate new insights is becoming more complex and time‐consuming.”
KnetMiner does all the hard work for you – scanning over 5 million relationships from across a range of biological data sources, scoring all evidence and displaying the links in easy to understand knowledge graphs.
Aimed primarily at plant and crop scientists, KnetMiner has already uncovered hitherto unknown genetic links between grain colour and pre-harvest sprouting in wheat. And whilst these two traits were anecdotally known to be related, until KnetMiner got to work, the possible mechanism remained elusive.
“KnetMiner has generated a potential linkage between grain colour and pre-harvest sprouting due to a grain colour gene interaction and suggested a new hypothesis between two traits, pre-harvest spouting and root hair density, that were not part of the initial investigation and previously thought to be unrelated.
“So as an example, by using KnetMiner, a researcher can discover the possibility that grain colour gene mutants might have more root hairs and higher nutrient and water absorption, which is what’s causing early germination of the grain. This can then be tested experimentally.”
KnetMiner has been used by the academic community for some time now, but it has recently caught the attention of the commercial plant breeding community.
A consortium of European plant breeding companies, VLPB, recently evaluated the value of KnetMiner to their businesses. Working together with the team at Rothamsted Research, the proof of concept project included virtual workshops and knowledge exchange events on using KnetMiner for data integration, knowledge mining and gene discovery.
According to Dr Hassani-Pak, the link-up was an enormous success.
“The breeding companies have learned about the power of KnetMiner to accelerate gene discovery using an integrated and cross-species approach, and we have learned about the requirements of different breeding companies and how they wish to further optimise KnetMiner to better fit their business environments.”
KnetMiner 5.0 will incorporate several new features that were requested by these companies to simplify on-premises deployment and customisation, he added.
“Going forward our vision is to grow our knowledge graph and apply our technologies to make a real-life impact towards food security and improved nutrition.”
About Rothamsted Research
Rothamsted Research is the longest-running agricultural research institute in the world. We work from gene to field with a proud history of ground-breaking discoveries, from crop treatment to crop protection, from statistical interpretation to soils management. Our founders, in 1843, were the pioneers of modern agriculture, and we are known for our imaginative science and our collaborative influence on fresh thinking and farming practices.
Through independent science and innovation, we make significant contributions to improving agri-food systems in the UK and internationally. In terms of the institute’s economic contribution, the cumulative impact of our work in the UK was calculated to exceed £3000 million a year in 20151. Our strength lies in our systems approach, which combines science and strategic research, interdisciplinary teams and partnerships.
Rothamsted is also home to three unique resources. These National Capabilities are open to researchers from all over the world: The Long-Term Experiments, Rothamsted Insect Survey and the North Wyke Farm Platform.
We are strategically funded by the Biotechnology and Biological Sciences Research Council (BBSRC), with additional support from other national and international funding streams, and from industry. We are also supported by the Lawes Agricultural Trust (LAT).
For more information, visit https://www.rothamsted.ac.uk/; Twitter @Rothamsted
1Rothamsted Research and the Value of Excellence: A synthesis of the available evidence, by Séan Rickard (Oct 2015)
The Biotechnology and Biological Sciences Research Council is part of UK Research and Innovation, a non-departmental public body funded by a grant-in-aid from the UK government.
BBSRC invests in world-class bioscience research and training on behalf of the UK public. Our aim is to further scientific knowledge, to promote economic growth, wealth and job creation and to improve quality of life in the UK and beyond.
Funded by government, BBSRC invested £469 million in world-class bioscience in 2016-17. We support research and training in universities and strategically funded institutes. BBSRC research and the people we fund are helping society to meet major challenges, including food security, green energy and healthier, longer lives. Our investments underpin important UK economic sectors, such as farming, food, industrial biotechnology and pharmaceuticals.
More information about BBSRC, our science and our impact.
More information about BBSRC strategically funded institutes
The Lawes Agricultural Trust, established in 1889 by Sir John Bennet Lawes, supports Rothamsted Research’s national and international agricultural science through the provision of land, facilities and funding. LAT, a charitable trust, owns the estates at Harpenden and Broom's Barn, including many of the buildings used by Rothamsted Research. LAT provides an annual research grant to the Director, accommodation for nearly 200 people, and support for fellowships for young scientists from developing countries. LAT also makes capital grants to help modernise facilities at Rothamsted, or invests in new buildings.