Welcome to T3/Oat

This is the SANDBOX site for T3/Oat. The Sandbox can be used to test the addition of new data to T3/Oat. Data added to this site will be periodically cleared and reset to match the main production version of T3/Oat. For more information on adding data to the Sandbox and submitting it to the production site, see the submitting data sections below.


T3/Oat is the repository of oat phenotype and genotype data for the Global Oat Genetics Database, a project initiated in January 2014. For more information see the Oat Global website. The database was developed at the website triticeaetoolbox.org/oat. That website was archived in Mar 2020 and all the data was moved to this current site.


Data Usage Policy

The data on this database is shared according to the Toronto agreement. Click here to view the full data usage policy.


Citation

If data on The Triticeae Toolbox was relevant to analyses or findings that you publish, please cite:

Nicolas Morales, Jean-Luc Jannink, Clay L. Birkett, David J Waring, Lukas A Mueller, et. al., Breedbase: a digital ecosystem for modern plant breeding, G3 Genes|Genomes|Genetics, Volume 12, Issue 7, July 2022, jkac078, https://doi.org/10.1093/g3journal/jkac078

If you have data to publish in our database, please submit the data using oat-sandbox. Then, once the data has been loaded in the production database you should use the trial id and dataset id as references in your publication. If you have multiple data submissions that are related, please create a "Dataset" using the wizard, use the wizard again make the Dataset Public, then list the dataset id as a reference. The following are examples of how to cite your data.

data typenamecitation
Phenotype trial1RS-Dry_2012_Davishttps://wheat.triticeaetoolbox.org/breeders/trial/7658
Genotype project2012_SRWW_ElitePanelhttps://wheat.triticeaetoolbox.org/breeders/trial/2780
Genotype protocolInfinium 90Khttps://wheat.triticeaetoolbox.org/breeders_toolbox/protocol/70
Breeding ProgramAllele Based Breeding Cooperativehttps://wheat.triticeaetoolbox.org/breeders/program/6208
Breeding Program folderABB Midhttps://wheat.triticeaetoolbox.org/folder/6210
DatasetTinker QTL 2021https://oat.triticeaetoolbox.org/dataset/18683




Future Workshops

We're collecing names and emails of those that are interested in attending future T3/Breedbase workshops on various topics such as using Android Field Book, Seedlots, Barcodes, or any other topic you may be interested in learning more about. Fill out the Virual Workshop Interest Form if you may be interested in attending a future workshop. Once we have enough interest in a particular topic, we'll reach out to everyone to schedule a date.



News

Scab Forum Presentation

Dec 5, 2022

The presentation of T3/Breedbase given at the 2022 Wheat & Barley Scab Forum can be found here. It includes information about the main features of T3/Breedbase, a general overview of creating phenotype upload templates, and highlights some of T3/Breedbase's advanced features (such as Seedlots and Barcodes).

PepsiCo v2 assembly

May, 2021

Speaking of Oats...

February 26, 2020

T3 gave the January Speaking of Oats webinar organized by Oat Global and the Oat Newsletter, where we discussed practical applications of T3/Breedbase for the oat community and an overview of adding and extracting data from the new database.

A video recording of the webinar is now available on YouTube and a transcript of the Q&A session (PDF) is available from the Oat Newsletter.

Breedbase Workshop Notes & Videos

September 10, 2020

T3 hosted a practical remote workshop demonstrating the process of uploading field trial data to the database. Notes from that workshop, which include step-by-step instructions on how to upload a sample dataset, are now available.

Video recordings of the workshop are available on the Breedbase YouTube Channel.

Scab Forum Presentation

Dec 9, 2019

The presentation (with step-by-step screenshots of the demos) of T3/Breedbase given at the 2019 Wheat & Barley Scab Forum can be found here.

Accessions Loaded

Dec 16, 2019

Accession entries have been created for all ~24,000 accessions that were in T3/Classic. Accessions have associated breeding programs, synonyms and GRIN ID numbers.



Templates

Blank Upload Templates

Below are blank upload templates for each data type.


Sample Templates

Generate a set of sample templates for new accessions, locations, trials, and trait observations. These templates contain all new data in properly formatted templates that can be used to practice uploading each data type to the sandbox.

  1. Generate your set of sample templates
  2. Follow the Guided Phenotype Upload Workflow to upload the template for each data type

Example Templates

Below are example templates generated for demo wheat trials from a 2020 workshop. You can use these files to see how the templates are properly formatted.


For more detailed instructions, see the Detailed Phenotype Upload Instructions



Explore T3/Oat

 Register

To view most of the data on T3/Oat, you'll first need to create a free account.


 Login

If you already have an account, login to get full access.

Use the Quick Search to find an Accession, Trial, Trait, etc by name:



Use the Search Wizard to explore the database or search individual data types:



Explore Experiments in the Search Wizard:

You must first log in to view the lists of experiments...




Submit Phenotype Data

To submit phenotype data to T3/Oat follow these three general steps:

Step 1: Create Upload Templates

Data submitted to T3/Oat should be in the format of the upload template for the data type you are submitting. View the detailed upload instructions for specific information on each data type.

Step 2: Add Data to Sandbox

Once you have your upload templates, you can test-load them on this Sandbox site to check for any errors.

Step 3: Submit Trial Data

If your trial data has been successfully added to the Sandbox you can submit your trials directly to the production site by clicking the Submit Trial button on the trial detail page.

If your data has not been added to the Sandbox or if you would prefer to submit your files directly to the production site, you can submit your individual upload templates or data files to us using the Phenotype Submission Form.





Submit Genotype Data

Please Contact Us if you have genotype data you would like to submit to T3/Oat.




User Guides

New to T3/Oat?

View the comprehensive Documentation from the Breedbase team to learn about available features or watch the detailed Video Tutorials.





T3/Oat is open source software and available under the MIT License and may be downloaded from GitHub.