Public Release:  Researchers develop free online database for soybean studies

Digital infrastructure can dramatically change the way researchers conduct their experiments

University of Missouri-Columbia

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IMAGE: Joshi developed SoyKB, a free online database that assists international researchers, scientists and farmers to solve questions encountered in soybean research. view more

Credit: MU News Bureau

COLUMBIA, Mo. - In the era of "big data," many scientific discoveries are being made without researchers ever stepping foot in traditional laboratories. Often, data from numerous experiments is gathered and disregarded, with only the desired results analyzed. Now, researchers at the University of Missouri have developed the digital infrastructure needed to store previously disregarded data to take plant science to the next level. The Soybean Knowledge Base (SoyKB), a free online data resource, allows collaboration among international researchers, scientists and farmers to solve questions encountered in soybean research.

"Researchers essentially deposit their results from experiments into the database, and high capacity computer systems crunch the numbers to help determine results," said Trupti Joshi, assistant research professor in computer science at the College of Engineering at MU. "Their experiments become a part of the bigger picture allowing future researchers to narrow their own results."

Highly collaborative in nature, SoyKB uses computational methods developed by computer science engineers that can be used for many disciplines, such as health sciences, animal sciences, physics and genetics. Additionally, a 3D-protein modeling tool available at the website assists with researchers studying drug design. Pharmaceutical companies may test hypotheses and, in some situations, the proposed drug may yield the expected results--formulated solely by data analysis making drug design more cost effective.

"Humans only can look at so many lines in an excel spreadsheet--then it just kind of blurs," said Gary Stacey, collaborator on the project, an investigator in the MU Bond Life Sciences Center and professor of plant sciences in the College of Agriculture, Food and Natural Resources. "We need these kinds of tools to be able to deal with this high-volume data. With this database, all the data is deposited and available so something that's not valuable to me may be valuable to somebody else."

Joshi is a valued resource to the finished product because she has both a biology degree and a computer science background, or a "foot in each camp," Stacey said.

"SoyKB has turned out to be a very good public resource for the soybean community to cross reference and check the details of their findings," Joshi said. "It can be really difficult for biologists to handle the large scope of data by themselves, and this tool allows researchers to focus more on the biology."

SoyKB is a part of the Obama Administration's $200 million "Big Data" Initiative, a program that works to improve the ability to extract knowledge and insight from large and complex collections of digital data and promises to help solve some of the nation's most pressing challenges. The progress of SoyKB was presented at the International Conference on Bioinformatics and Biomedicine in Shanghai in December, 2013. The ongoing project is funded by grants from the National Science Foundation.

Joshi's research highlights the Food for the Future area of The Mizzou Advantage, an initiative that fosters interdisciplinary collaboration among faculty, staff, students and external partners to solve real-world problems in four areas of strength identified at the University of Missouri. The other three areas are Sustainable Energy, Media for the Future, and One Health/One Medicine.

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Joshi's most recent publication, "Major Soybean Maturity Gene Haplotypes Revealed by SNPViz Analysis of 72 Sequenced Soybean Genomes," was published in PLOS One.

Editor's Note: For longer versions of this story, please visit: http://decodingscience.missouri.edu/2014/06/soykb-leading-the-convergence-of-wet-and-dry-science-in-the-era-of-big-data/, or http://engineering.missouri.edu/2014/06/assistant-professor-manages-online-database-for-soybean-studies/.

Story Contact(s):

Jeff Sossamon, sossamonj@missouri.edu, 573-882-3346

Paige Blankenbuehler, paigeblankenbuehler@mizzou.edu, 573-882-4544

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