The Triticeae Toolbox
Public breeding databases for wheat, oat, and barley
View Databases
Photo by FreePik
View Databases
Photo by FreePik
A curated public wheat database, where any user can access and download data
wheat.triticeaetoolbox.org
A sandbox version of the public wheat database, where any user can upload data to test out the database
wheat-sandbox.triticeaetoolbox.org
A private wheat database available to WheatCAP participants. New accounts have to be approved by the website administrators.
wheatcap.triticeaetoolbox.org
The original T3 wheat database with data up to January 2020
triticeaetoolbox.org/wheat?old=1
A curated public oat database, where any user can access and download data
oat.triticeaetoolbox.org
A sandbox version of the public oat database, where any user can upload data to test out the database
oat-sandbox.triticeaetoolbox.org
The original T3 oat database with data up to March 2020
triticeaetoolbox.org/oat?old=1
Pedigrees of Oat Lines, a simple interface to a database that contains information about oat varieties and their pedigrees.
triticeaetoolbox.org/POOL
A curated public barley database, where any user can access and download data
barley.triticeaetoolbox.org
A sandbox version of the public barley database, where any user can upload data to test out the database
barley-sandbox.triticeaetoolbox.org
The original T3 barley database with data up to June 2020
triticeaetoolbox.org/barley?old=1
The Triticeae Toolbox (T3) is the web portal for data generated initially by the Triticeae Coordinated Agricultural Project (TriticeaeCAP), and now by WheatCAP. T3 is funded by the National Institute for Food and Agriculture (NIFA) of the United States Department of Agriculture (USDA). T3 contains DNA marker, phenotypic, and pedigree data from wheat, oat, and barley germplasm from public sector breeding programs across the United States. The purpose is to integrate rapidly expanding DNA marker and phenomic data with traditional phenotypic data, providing access to powerful joint predictive analyses mapping genotype to phenotype and enabling breeders to collaborate to accelerate gains from selection. T3 also links to related genomic and crop diversity databases (GrainGenes, Gramene, GRIN, and D2S) for functional analyses to identify causal polymorphisms and networks affecting phenotypes.
The Triticeae Toolbox is based off of breedbase, developed by the Lukas Mueller lab at The Boyce Thompson Institute. The source code for both is publicly available on GitHub, where anyone can view or download the code. Docker images are perodically built and published to Docker Hub for consistent deployment across different systems.
The Synonym Search Tool is a BrAPI (Breeding Application Programming Interface) compatible app that can be used to find germplasm in any BrAPI-compliant database (such as T3 or any other breedbase instance) that match or are similar to the user-provided list of germplasm names. This tool is used in an effort to reduce the number of duplicate germplasm entries with variations in names.
The standalone search tool is available at: https://synonyms.triticeaetoolbox.org. In addition, the search tool is integrated into the accession and trial uploads on T3 so that every new germplasm entry in T3 is first searched against existing entries before being added to the database.
The source code for the search tool is availabe on GitHub.
The T3 BrAPI R package includes some simple wrapper functions for making HTTP BrAPI requests in R. It includes information required to connect to a T3 instance via BrAPI as well as functions for making GET, POST, and PUT requests using BrAPI endpoints. While the core BrAPI functions will work with any BrAPI-compliant database, the package also includes some breedbase-specific functions, such as interacting with the breedbase Search Wizard directly in R.
For more information on how to install the package and its usage, view the package's README on GitHub.
The Breedbase R package is a set of classes and functions that represent each of the major data types on T3 / breedbase (Accessions, Locations, Trials, Observations, etc). These classes and functions can then be used to generate upload templates used to add new data to the database. These tools are helpful when parsing existing data into files to be uploaded to a breedbase database.
For more information on how to install the package and its usage, view the package's README on GitHub.
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