Seeing the forest through the trees
KNOXVILLE, Tenn. – Autumn adorns trees with richly hued leaves and clusters of nuts or other presentations of seeds for the future of tree species. Meg Staton, a research scientist with a penchant for big data, looks at these trees and sees thousands upon thousands of data points to be compiled for analyses.
Staton is an assistant professor of bioinformatics with the University of Tennessee Department of Entomology and Plant Pathology, and she is also a co-principal investigator in a three-year, $3-million grant by the National Science Foundation to develop a user-friendly interface that will help forest scientists everywhere record and share their genomic data for various tree species. As part of the grant, which was awarded earlier this year, researchers from four universities are working with the U.S. Forest Service's Southern Research Station to accelerate both basic discovery and improvement of important agronomic and silvic traits in tree crops.
Dorrie Main, a professor at Washing State University (WSU), is principal investigator for the project, but Staton is leading the UT Institute of Agriculture portion of the effort, which totals more than $623,000.
The project team proposes to "create a model 'ecosystem' of community databases that can inter-communicate and will also provide big data analysis tools utilizing common controlled vocabularies." Just what is big data? In the case of this project, big data is the collection of massive amounts of information regarding the genomics of trees. Staton says the sets of information are so large that a single researcher would have difficulty storing and analyzing all the information for a single plant or for a collection of plants or species.
"There are so many sources of public data available, but they can be disorganized and difficult to find. We plan to link the many different types of open research data for trees together as richly annotated data sets," Staton said. "With access to new data sets and enhanced computing capabilities through the web, researchers can build on previous work to enhance selection, breeding and management of trees for a variety of goals, such as agronomic efficiency gains and conservation of native species.
A previous grant allowed the researchers, including Staton, to develop the cyberinfrastructure for the Tripal software which allows for flexible access to information already existing for forest and fruit trees. Once complete, Tripal will enable scientists and the public to easily access information about trees, tree genetics, sequences of tree genomes and other information housed in specialized tree breeding and research community databases. Staton adds that there may soon be a social media component of the highly technical database. "We're working to make the Tripal cyberinfrastructure interface compatible with certain mobile apps that allow users to geo-tag tree species on social media. Citizens are valuable allies in protecting our forests, and it's also a great way to engage youth with the outdoors and our beautiful local trees," she said.
The grant will also enable adoption of these new data-sharing capabilities through development of educational online modules that can train scientists to effectively query existing data, upload new data, assign metadata and perform custom analyses.
The investigators also hope that this project will help raise public awareness of the importance of healthy trees as well as promote stewardship of our forests. They write in their grant proposal abstract that healthy trees are of critical importance to a productive, sustainable planet and the U.S. economy.
Other participating researchers in the project are Sook Jung and Stephen Ficklin from WSU, Jill Wegrzyn from the University of Connecticut and Albert Abbott from the University of Kentucky.
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