Welcome to T3/Oat

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.


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.


Submission

Use the Phenotype Submission Form to submit your data to the curators for inclusion in T3/Oat.


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

Phenotype data can be submitted to T3/Oat in two ways:

Submitting files directly to us

If you have upload templates that you think are properly formatted or data files that are not formatted as upload templates, you can submit the files directly to use for inclusion in the production site by submitting them to us through the Phenotype Submission Form.

   Phenotype Submission Form

Using the Sandbox

When using the sandbox, you create upload templates that contain the trial information. Then, you upload those templates to the Sandbox to check for any errors. When the trial has been successfully added you can use the Submit Trial function to submit the trial directly to us for inclusion in the production site. Visit the T3/Oat Sandbox for more information.

   Visit the T3/Oat Sandbox


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.