2023 WheatCAP Workshop

Dates / Times

:calendar: Mon, Feb 6 - Thu, Feb 9th
Fri, Feb 10th is available for extra help / questions

:clock1: 12 PM EST / 9 AM PST --> 2 PM EST / 11 AM PST

:video_camera: Zoom Link

Contact Info

If you have any questions throughout the Workshop or afterwards, feel free to reach out to us:

T3/Breedbase Databases:

Phenotype Upload Instructions:

Synonym Search Tool: https://synonyms.triticeaetoolbox.org

Field Book App Instructions: https://wheat.triticeaetoolbox.org/static_content/files/FieldBookAppT3.pdf

Blank Upload Templates

:paperclip: Location Template
:paperclip: Accession Template
:paperclip: Trial Template (trial information and plot layout)
:paperclip: Phenotype Template (trait observations)

Video Recordings


Below is an overview of each day’s assignment and new material we’ll be covering. See the details for each day below for more information.

Each Assignment should be completed BEFORE the day it’s assigned.

:one: Day One


New Topics

:two: Day Two


New Topics

:three: Day Three


New Topics

:four: Day Four


New Topics

:one: Day One

:notebook: Assignment

Throughout the workshop, we’ll be helping you load your own trials into T3/Breedbase. In order to do this, you’ll need to get together the required information for loading your trials into the database. This includes:

You’ll be uploading your trials to the T3/Wheat Sandbox. If you don’t already have an account on the Sandbox, make sure to create one before the workshop begins. To create an account:

  1. Go to https://wheat-sandbox.triticeaetoolbox.org
  2. Click the “Register” button in the top right of the Toolbar
  3. Fill out the new account form
  4. You will get an email from noreply@triticeaetoolbox.org with a link to verify your email address.
  5. Make sure you can login with your new account

:information_source: Each version of T3 (production, sandbox, WheatCAP, etc) has its own database with its own accounts. You’ll need to create an account on each database you want to use.

:sparkles: New Topics

1) Databases

2) Locations

Check if any of your Locations already exist

Location Metdata

Make sure you have all of the required information for any new Locations

:memo: Location Template Information

Adding a Single Location on the Map

If you only have a small number of Locations to add, you can add them individually using the map on the website

Adding Multiple Locations with Upload Template

If you have multiple Locations to add, you can submit them all using the Location upload template

3) Accessions

Check if your Accessions already exist in the Database

Use the Synonym Search Tool to find potential matches

This tool is now integrated into the Accession and Trial uploads, so it’s not required to use the Synonym Search Tool separately. However, doing a separate search yourself gives you more control over the options it uses and you can find issues with Accession names before you try to upload a file.

Accession Metadata

Make sure you have all of the required information for any new Accessions that need to be added to the Database

:memo: Accession Template Information

Adding new Accessions with the Upload Template

Fill out the Accession Upload Template for any new and/or updated Accession entries

Upload your completed Accession Upload Template

Adding Pedigrees

Purdy Pedigree strings can be added in the Accession Upload Template

:two: Day Two

:notebook: Assignment

Follow the instructions from Day One to upload your own Locations and Accessions to the T3/Wheat Sandbox.

You should create/upload a Location for each field trial location.

You should upload any missing Accessions that are not already in the database that are used in your field trials.

:sparkles: New Topics

A Trial on T3/Breedbase is a planting at a single location in a single year. This means, you’ll need to create a new Trial for each new location and/or year.

An Experiment is a grouping of related Trials from the same Breeding Program. (Experiments are created by putting related Trials in the same folder on the Manage > Field Trials page).

1) Field Layouts

Multi-Trial Upload Template

The Multi-Trial Upload Template can be used to upload one or more Trials to the database. Each row in the template corresponds to one plot in a single trial. Add a new row to the template for each plot in the trial. If you’re uploading more than one Trial, you can add additional rows to the template below the first Trial.

:information_source: Keep the plots/rows from the same Trial grouped together - the uploader will process one Trial at a time and expects the plots to be next to each other in the file.

Trial Naming Conventions

The Database includes Trials from many different Breeding Programs and the Trial name must be unique across all Trials for all Breeding Programs in the Database. Thefore, we recommend including these three components in the trial name (separated by a _):

For example: CornellMaster_2007_McGowan, 5STADV_2001_Urbana

Plot Naming Conventions

Each Plot within a Trial also needs to have a globally unique name. This is what you use when you upload trait observations (you’ll reference the Plot by its unique name). The easiest way to create a unique Plot name is to combine the Trial name with -PLOT_{plot number}.

For example: CornellMaster_2007_McGowan-PLOT_101, CornellMaster_2007_McGowan-PLOT_102.

You can use the CONCAT function in Excel to combine the Trial Names and the Plot Numbers to generate the Plot Names.

For example: =CONCAT(A2, "-PLOT_", O2)

Plot Position Coordinates

Each plot can have a row and column position within the field. This information is critical in knowing the spatial layout of the plots within the field and is required for processing drone imagery (via UASHub). Each plot should have its own unique row/col pair (there should only by one plot at each position).

Template Structure

The Multi-Trial Upload Template contains trial-level metadata (such as the Trial name, planting date, etc). This information is the same for all plots in the Trial, so each row/plot from the same Trial should have the same values. The trial-level columns are on the left.

The Upload Template also contains plot-level metadata (such as the Plot name, Accession used in the plot, etc). This information will be different for each plot in the Trial, so each row/plot will have a different value. The plot-level columns are on the right.

Trial Metadata

Make sure you have all of the required metadata for each new Trial. All of the associated Breeding Programs, Locations, and Accessions must already exist in the Database before you can upload the Trial.

:memo: Multi-Trial Template Information

Trial Properties

The following properties relate to the trial:

Plot Properties

The following properties relate to a plot:

Upload your completed Multi-Trial Upload Template

Once you’ve filled out your Multi-Trial Upload Template, you can upload it to the Database:

2) Trait Observations

All of the Traits in T3/Breedbase are stored in a collaborative trait ontology (available via cropontology.org). This means that each Trait in the Database has an official name and identifier which is used to reference the Trait and is linked with a specified trait definition, method description, and unit/scale of measurement.

To upload your own trait observations, you’ll need to match your traits with those stored in the database. You’ll need to make sure the trait definition, method description, and unit/scale are all the same. If the only difference is the unit/scale, then we ask that you convert your values to match the unit/scale of the database trait - this reduces the number of similar traits and keeps the data more comparable across Breeding Programs.

If you have a trait that does not have a corresponding match in the Database, let us know and we can work on adding it to the trait ontology.

To search the existing Traits

When you find a matching trait, you will need to know its name and ID when you are ready to upload observations.

If you want to save your Traits in the Database, you can create a List of traits to use later.

Composed Traits

T3/Breedbase currently only allows one value to be stored for each combination of plot and trait. In order to save multiple values for a trait (such as for a timeseries), you’ll need to associate each value with a “Composed Trait” - which is a combination of a base trait and a time term.

For example, if you’re measuring Canopy Cover with multiple drone flights, Canopy Cover - UASHub - % will be the base trait and the time term will be the Julian Day (1-365: 1=Jan 1st, …, 365=Dec 31st) of the observation. This will give you a different trait for each day:

Drone Trait Lookup

To make it easier to calculate the Julian Day for a Date and to lookup the matching Composed Trait Name and ID, you can use the Drone Trait Lookup tool:

Observation Upload Template

Once you have found the Database Traits that correspond to your Traits, you can create the Observation Upload Template

In order to associate the observations with specific Plots, you’ll use the unique Plot Name for each plot (these were created in the Multi-Trial Upload Template)

:memo: Phenotype Observation Template Information

We’ll be using the simple phenotyping spreadsheet format. This format has one required column for the plot name followed by a column for each observed trait.

The column headers are:

Each row in the Observation Upload Template corresponds to a single Plot and each column corresponds to a single Trait.

:information_source: The Plots from more than one Trial can be included in the same Observation Upload Template.

:information_source: The cells for missing / unobserved values should be left blank. If you’re exporting from another program, make sure it doesn’t fill in NA or .'s for missing values.

Example Observation Upload Template:

observationunit_nameGrain yield - kg/ha|CO_321:0001218Grain test weight - g/l|CO_321:0001210FHB incidence - %|CO_321:0001149FHB severity - %|CO_321:0001440FHB DON content - ppm|CO_321:0001154

Once you have a filled-in Observation Upload Template, you can upload it to the Database:

:three: Day Three

:notebook: Assignment

Follow the instructions from Day Two to upload your own Trials to the T3/Wheat Sandbox.

If you have any observation data at this point, you can add the observations to your Trials. If not, you can match up all of your traits to the Trait names and IDs in the database.

:sparkles: New Topics

1) Lists

A List is a collection of items of a single data type (such as Accessions, Trials, Traits, etc). They can be saved so you have easy access to them and they can be made public so others can use them.

Creating a List

There are a number of different ways to create a List and add items to a List


Lists are used throughout the website whenever a collection of Items is needed, such as selecting data for download or using data in an analysis tool

2) Data Aggregation, Subsetting, & Download

3) PHG / Imputed Data

:four: Day Four

:notebook: Assignment

For this assignment, you’ll be trying to find data in T3 that is related to Accessions in your Breeding Program.

First, find some Accessions from your Breeding Program that might have had data submitted to T3 (such as past phenotyping trials or data submitted to a genotyping lab).

Next, put your Accession names through the Synonym Search Tool to try to find matching Accessions in the database.

Then, create a List of the matching Accessions and use the List to download some related phenotype and/or genotype data.

:sparkles: New Topics

1) Android Field Book

2) Seedlots

A Seedlot represents a single packet of collected seed

A Seedlot has the following properties:


Creating Seedlots

Using Seedlots

3) Barcodes

Barcodes can be generated for:


Use Cases:

Custom Label Designer:

The Custom Label Designer is available from the Manage > Barcodes page and clicking the Design Custom Barcode button at the top right of the page.

  1. Choose Data Source

    • Field Trial
    • Genotyping Plate
    • List (can be a List of any data type)
  2. Select Page Size & Label Dimensions

  3. Add Components to Label

    • Barcode
    • Additional Text
  4. Download PDF of Labels

4) Submitting Genotype Data

  1. Requirements
    • accessions
    • reference genome
    • file format
    • protocol, project
  2. Loading through website
    • check for accessions not in T3
    • check chromosome name, ref/alt, and ID
    • Define genotype project
    • Define genotype protocol
    • Select file