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About T3

Project Description

The Triticeae Toolbox (T3) is the web portal for data generated by the Triticeae Coordinated Agricultural Project (T-CAP), funded by the National Institute for Food and Agriculture (NIFA) of the United States Department of Agriculture (USDA). It also contains data from US Uniform Regional Nurseries, supported by the US Wheat and Barley Scab Initiative. The database was initially developed as The Hordeum Toolbox (THT) to hold barley data generated by the Barley CAP project (2006-2010). T3 Barley hods data generated for Hordeum vulgare L. T3 Wheat holds data generated for Triticum spp. T3 Oat holds data generated for Avena. All are being enhanced in database performance, community curation and user tools. T3 contains germplasm line information, pedigree, genotype and phenotypic data from breeding programs participating in the CAP and core germplasm collections maintained by the USDA National Small Grains Collection.

Dataset Acknowledgments

9K wheat iSelect assay

The 9,000 SNP wheat iSelect assay was designed by research groups funded by the USDA National Institute of Food and Agriculture (grant CRIS0219050; PI: E. Akhunov; co-PIs: S. Chao, G. Brown-Guedira, D. See, M. Sorrells) and the Grains Research and Development Corporation (GRDC), Australia (PI: Matthew Hayden). The details of assay design can be obtained from the USDA wheat SNP development project and International Wheat SNP Working Group websites.

T3 Team

NameAffiliationRole
Jean-Luc JanninkUSDA-ARS, NAA, RWHCAH, Ithaca, NYProject coordinator
Mark SorrellsCornell University, Ithaca, NYProject coordinator
Clay BirkettUSDA-ARS, NAA, RWHCAH, Ithaca, NYDatabase programming and development
Clare SaiedCornell University, Ithaca, NYData curator
Dave MatthewsCornell University, Ithaca, NYDatabase development, GrainGenes collaborator
Shiaoman ChaoUSDA-ARS Biosciences Research Lab, Fargo, NDSNP data production and curation
Peter BradburyUSDA-ARS, NAA, RWHCAH, Ithaca, NYPedigree information and links to TASSEL
Mike BonmanUSDA-ARS, Aberdeen, IDGRIN collaboration
Harold BockelmanUSDA-ARS, Aberdeen, IDGRIN collaboration
Tim CloseBotany and Plant Sciences
University of California
Riverside, CA
Assembly and SNP context information from HarvEST: Barley
T-CAP ParticipantsThroughout the U.S.A.Data collection and contribution

THT Alumni

NameAffiliationRole
Julie A. DickersonElectrical and Computer Engineering, Iowa State UniversityPrincipal Investigator
Roger P. WiseUSDA-ARS
Department of Plant Pathology
Iowa State University
Principal Investigator
Jennifer KlingDept. of Crop and Soil Science Oregon State UniversityPhenotype and pedigree data curation
Shreyartha MukherjeeBioinformatics and Computational Biology, Iowa State UniversityDeveloper/Bioinformatics
Kartic RameshComputer Science, Iowa State UniversityDeveloper
Gavin MonroeSoftware Engineering, Iowa State UniversityDeveloper
Ethan WilderComputer Engineering, Iowa State UniversityDeveloper
Yong HuangBioinformatics and Computational Biology, Iowa State University Developer/Bioinformatics

Collaborators

The James Hutton Institute Development Team (David Marshall, Paul Shaw)
PLEXdb Development Team at Iowa State University (Ethy Cannon and Sudhansu Dash)
Gramene Database (Doreen Ware)
GrainGenes Database (David Matthews) USDA/ARS, Cornell University

Software availability

The T3 software is available under the GNU General Public License (LICENSE) and may be downloaded from GitHub.
It requires Linux, Apache, MySQL, and PHP. Details are in the INSTALL document.
A list of recent changes to the T3 software are in the Change Log document.
The database schema in .sql format is here. Graphical diagrams are available in MySQL Workbench (.mwb) format and .png format.

In 2009 the Toronto International Data Release Workshop agreed on a policy statement about prepublication data sharing. Accordingly, the data producers are making many of the datasets in T3 available prior to publication of a global analysis. Guidelines for appropriate sharing of these data are given in the excerpt from the Toronto Statement.

I agree to the Data Usage Policy as specified in Toronto Statement.