T3/Oat

Guided Phenotype Upload Workflow

Intro
Breeding Program
Locations
Accessions
Trials
Observations
Finish

Introduction
This workflow will guide your through the basic steps required for adding one or more phenotyping / field trials to the database:
- Ensuring the Breeding Program(s) exist
- Adding new Locations where the trials were performed
- Adding new or updated Accessions (germplasm lines)
- Creating Trials and their plot layouts
- Adding Phenotype Observations to the plots
Download Templates Download Templates
Blank Upload Templates

Below are blank upload templates for each data type
Example Templates

Below are example templates generated for demo trial data from a 2020 workshop. You can use these files to see how the templates are properly formatted.
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 database.
- Generate Sample Templates
Breeding Program(s)

Trials are associated with a single Breeding Program. Before a Trial can be added, the Breeding Program must already exist in the database.

Check the table below to see if your Breeding Program has already been created.

Breeding Programs:

Name Description

If your Breeding Program exists:

Continue to the next step

If your Breeding Program does not exist:
1. Go to the Manage > Breeding Programs page
2. Click the Add New Program button at the bottom of the page to add your Breeding Program to the database
Detailed Instructions Detailed Instructions
Breeding Program

All data (such as Accessions and Trials) are associated with a particular Breeding Program. Generally, we have a Breeding Program for each University / Institution that submits data to the database. For cooperative / nursery trials, there may be a Breeding Program created specifically for the nursery (ex: Uniform Oat Performace Nursery). Trials performed for the nursery are associated with the nursery Breeding Program in order to keep them grouped together in the database.
1. Make sure your Breeding Program exists in the Database
  
  View existing Breeding Programs: Manage > Breeding Programs
2. If it is not listed, add it to the Database:
  
  Go to the Manage > Breeding Programs page
  
  Click the Add New Program button at the bottom of the page
  
  Fill out the Breeding Program name and description
  
  View the Managing Breeding Programs manual page for more information.

Locations

Each Trial needs to be associated with a single Location and the Location needs to exist in the database before adding a Trial. Most of our trials are associated with a location of the closest town to the field site. However, more specific locations can be used (such as a separate location for each field).

Check the table below to see if the Location(s) of your Trial(s) have already been created.

Locations:

Name	Abbreviation	Country	Trials

If your Location(s) exist:

Continue to the next step

If your Location(s) do not exist:

Go to the Manage > Locations page
Click the [Upload New Locations] link in the top right corner of the page to upload a Locations Excel Template

Detailed Instructions

Blank Location Template

Locations

A phenotyping trial must be linked to a specific location. Generally, the location of a trial is set as the closest town to the actual field site. However, more specific locations can be added (such as separate locations for each farm and/or field).

T3/Oat uses the following naming conventions for the Location name and abbreviation:

Type of Location	Name Convention	Name Example	Abbreviation Convention	Abbreviation Example	Location Type
Town (closest to field site)	{Town name}, {2-letter State / Province abbreviation}	Ithaca, NY	{First 3 letters of town name}{2-letter State / Province abbreviation}	ITHNY	Town
Farm (a specific farm site, but an unknown / unspecified field at the farm)	{Town name}, {2-letter State / Province abbreviation} - {Farm name}	Ithaca, NY - Caldwell	{First 3 letters of town name}{2-letter State / Province abbreviation}-{First 3 letters of the Farm name}	ITHNY-CAL	Farm
Field (a specific field within a farm site)	{Town name}, {2-letter State / Province abbreviation} - {Farm name} - {Field identifier}	Ithaca, NY - Caldwell - A	{First 3 letters of town name}{2-letter State / Province abbreviation}-{First 3 letters of Field name}-{Field ID}	ITHNY-CAL-A	Field
These are suggested naming conventions, but can be changed if there are conflicts with existing locations or a different abbreviation is more suitable for a specific Location.

Make sure the Location of your Trial(s) exist in the Database
- Use the Manage > Locations page to search for existing Locations.
If the one or more of your Locations don't exist in the database, you can add them by either:
- uploading a file of location information:
  - Go to the Manage > Locations page
  - Click the Upload New Locations link in the top right corner of that page
  - Create an Excel (.xls) file (Download blank template) with the specified headers
  - Upload the file
- selecting the location from the map:
  - Go to the Manage > Locations page
  - Scroll and zoom in on the map to the location
  - Click on the map where the location should be added
  - Click the Add Location link in the pop-up
  - Fill out the form with the Location properties
  - Click the Store Location Details button to save the Location
- View the Managing Locations manual page for more information.
Make sure your Breeding Program is associated with the location.
- In the Location Table on the Manage > Locations page, the Program column lists all of the Breeding Programs associated with each Location.
- If your Breeding Program is NOT associated with the Location:
  1. Find the location on the map
  2. Click the Edit link
  3. In the Program select box, ctrl-click / command-click your Breeding Program from the list to add it to the existing Breeding Programs already associated with the location.
  4. Click the Store Location Details button to save your changes.

Accessions

The contents of each plot must be associated with a single Accession (germplasm line). The Accession must exist in the database before a Trial can be created. Also, you must refer to the exact spelling and letter-case of the Accession's name (or synonym) in the database when creating the Trial.

We try very hard to avoid creating duplicate entries of an Accession based on variations in the spelling and/or characters used in the Accession name. Therefore, we highly recommend using the BrAPI Germplasm Search Tool to search for existing Accession entries in the database and any that match possible variations in spelling and/or punctuation.

Search for existing Accession entries:
- Search for exact matches of individual entries using the Search > Accessions and Plots page
- Search for exact matches of multiple entries using the Search > Bulk Search page
- Search for multiple entries (and variations in spelling and/or punctuation) using the BrAPI Germplasm Search Tool
If all of your Accessions already exist:

Continue to the next step

Add any new Accessions to the database:
1. Go to the Manage > Accessions page
2. Click the [Add Accessions or Upload Accession Info] link in the top right corner of the page
3. Select the Uploading a File tab to upload an Accessions Excel template
Detailed Instructions Detailed Instructions
Blank Acccession Template
Accessions

Each Accession (germplasm line) that is observed in a phenotype trial must have its own entry in the database. In addition, the line names used in your trial design must match the names (or synonyms) of the Accessions in the database.
1. Make sure your Accessions exist in the Database
  
  Use the Search > Accessions and Plots page to search for the Accessions in your trial (individually)
  
  Use the Search > Bulk Search page to find exact matches of multiple entries
  
  Use the BrAPI Germplasm Search tool to find matches of existing Accessions (or variations in spelling and/or punctuation) for all of the lines in your trial.
2. If one or more of your Accessions don't exist in the database, you can add them by uploading a file of Accession information
  
  Go to the Manage > Accessions page
  
  Click the Add Accessions or Upload Accession Info link in the top-right corner of that page.
  
  Click the Uploading a File tab
  
  Create an Excel (.xls) (Download blank template) file with the specified headers (Click Spreadsheet format for more info)
  
  When creating a spreadsheet of Accessions, a minimum of these columns should be filled in:
  
  accession_name: the unique name of the accession
  
  species_name: Triticum aestivum
  
  organization_names(s): The Breeding Program(s) that originated the Accession
  
  purdy_pedigree: The Purdy pedigree string for the accession (Female Parent/Male Parent)
  
  Upload the Accessions template
  
  View the Managing Accessions manual page for more information.

Trials

A Trial (a single location & year environment) must exist in the database before Trait Observations can be added. When a Trial is created, the folllowing information is added to the database:

Trial Metadata, such as:
- the Breeding Program that performed the Trial
- the Location
- the Design Type
- the Planting/Harvest Date(s)
Plot Metadata, such as:
- the Accession grown in the Plot
- Plot number
- Block number
- Rep number
- Whether or not the Plot is used as a control
- Row/Column position of the Plot within the field

Upload a Multi-Trial Upload Template:

Go to the Manage > Field Trials page
Click the Upload Existing Trial(s) button in the top right corner of the page
On Step 2, select the Multiple Trial Designs tab
Upload a Multi-Trial Excel Template

Detailed Instructions

Blank Multi-Trial Template Blank Single Trial Template

Trials

A phenotyping trial must exist in the database before the results can be added. The Trial contains information about its location, plot and field size, design type, planting/harvest dates, and plot layout. For trial mean data, create a Trial with one rep of Plots (one Plot for each Accession). Then, add the trial means as the trait value for each of the plots.

Trials and Plots must all have unique names in the database. T3/Oat uses the following naming conventions for Trials and Plots:

	Naming Convention	Examples
Trials	In order to create a globally unique name, it is best to include a Breeding Program-specific prefix and/or experiment code, the year of the trial, and the name of the Location.	UMOPN_2020_Urbana UIL_AYT_2020_Urbana
Plots	In order to create a globally unique name, we use the plot naming convention: {TRIAL_NAME}-PLOT{PLOT#}	UMOPN_2020_Urbana-PLOT1 UIL_AYT_2020_Urbana-PLOT1

A Trial can be added in multiple ways:

Option A - Using the trial design wizard: This will design a plot layout for you given lists of Accessions used as entries and controls, a trial design type, and layout parameters. To design a new trial:
1. Make sure you have the Accessions used as entries (and optionally as controls) in a List
2. Go to the Manage > Field Trials page
3. Click the Design New Trial button in the top-right corner
4. Fill out the Trial metadata form
5. Select the lists of Accessions for entries and optionally checks
6. Select the plot layout parameters
7. Review the generated plot layout
8. Save the Trial and its plot layout to the database
View the Trial Design manual page for more information on adding a trial using the trial design wizard.
View the Working with Lists manual page for more information on creating and managing lists

Option B - Uploading a plot layout spreadsheet for a single trial: This option can be used if you've already generated the plot layout and you can create a spreadsheet describing the plot layout for the trial. To upload an existing trial design:
1. Go to the Manage > Field Trials page
2. Click the Upload Existing Trial(s) button in the top-right corner
3. On Step 2, select the Single Trial Design tab
4. Create an Excel (.xls) file (Download blank template) that describes the plot layout with the specified headers (Click Single trial spreadsheet for more information). The following columns are required:
  - plot_name - must be unique across the database (ie: UEOPN_Urbana_2019-plot1)
  - accession_name - must match an existing Accession
  - plot_number - must be unique within this trial
  - block_number
  If you have private data included in your trial, you can add a 1 to the is_private column for plots to exclude from the database.
5. Fill out the Trial metadata form
6. Upload the plot layout template
7. Review any possible errors in the trial and/or its design
8. Save the Trial and its plot layout to the database
View the Trial Upload manual page for more information on uploading a trial design file.

Option C - Uploading a plot layout spreadhseet for multiple trials: This option can be used for uploading multiple trials at a time by generating a spreadsheet containing the trial metadata and plot layout information. This option does not require filling out the trial metadata form for each trial. To upload multiple existing trial designs:
1. Go to the Manage > Field Trials page
2. Click the Upload Existing Trial(s) button in the top-right corner
3. On Step 2, select the Multiple Trial Designs tab
4. Create an Excel (.xls) file (Download blank template) that includes the trial metadata and plot layout for each trial with the specified headers (Click Multiple trial spreadsheet for more information, including required columns and the data required for each column).
  If you have private data included in your trial, you can add a 1 to the is_private column for plots to exclude from the database.
5. Upload the trial design template
6. Review any possible errors in the trials and/or their design
7. Save the Trials and their plot layouts to the database

Trait Observations

Once the Trial(s) have been added to the database, Trait Observations can be added to the Plots within the Trial(s).

To add Trait Observations, you will need:
- The Plot Name (used when creating the Trial)
- The Trait Name of each observation (from the Search > Traits page)
- The Trait ID of each observation (from the Search > Traits page)
It is important to note the units/scale used by the trait in the database. If your observations were recorded using a different scale, you will need to convert them to the scale used by the database first.

File Format:
- The first column has the header observationunit_name and contains the Plot Name (or Subplot Name or Plant Name, but it is almost always going to be the Plot Name)
- Add an additional column for each trait being stored. The column header follows the format {Trait Name}|{Trait ID} and contains the trait values for each Plot. Unobserved plots should be left blank.
Upload a Trait Observations Template:
1. Go to the Manage > Phenotyping Results page
2. Click the [Upload Spreadsheet] link in the top right corner of the page
3. Change the Spreadsheet Format format to Simple
4. Upload a Trait Observations Excel Template
Detailed Instructions Detailed Instructions
Blank Simple Phenotypes Template
Phenotype Observations

Once a Trial has been created, phenotype observations can be added to the Trial. If you use the Field Book tablet app, you can create a file for recording your observations directly on Field Book. If you already have data, you can download a spreadsheet template specifically for the trial.
- Using Field Book:
  
  Go to the Trial detail page for your trial
  
  Go to the Search > Field Trials page or the Manage > Field Trials page
  
  Find your trial
  
  Click the name of your trial to open the Trial detail page
  
  Open the Upload Data Files section
  
  Click the Create Field Book button
  
  This file can then be used as a field layout file to collect data using the Android Field Book app
  
  After data collection: Click the Upload button next to Android Field Book Exported
  
  Additional files, such as images or raw data files can be uploaded in the Upload Additional Files section
- View the Using Field Book App section in the manual for more information on collecting field data using the Android tablet app.
- Uploading Existing Data:
  
  Create a list of Traits that were observed in your trial
  
  Go to the Trial detail page for your trial
  
  Go to the Search > Field Search page or the Manage > Field Trials page
  
  Find your trial
  
  Click the name of your trial to open the Trial detail page
  
  Open the Upload Data Files section
  
  Click the Create Spreadsheet button next to Phenotyping Spreadsheets
  
  Trait List: The list of Traits observed in this Trial
  
  Spreadsheet Format: Simple
  
  Data Level: Plots (for both plot-level data AND trial-mean data)
  
  For plot-level data: Observations at the individual plots can be recorded in each separate plot
  
  For trial-mean data: Trial means for each trait will be recorded as a single observation in one plot for each Accession
  
  This will create a template, for this specific trial, for adding phenotype observations to
  
  Once data has been entered into the template: Click the Upload button next to Phenotyping Spreadsheets to add the recorded observations.
  
  Additional files, such as images or raw data files can be uploaded in the Upload Additional Files section
- View the Uploading Spreadsheet Phenotypes manual page for more information on uploading phenotype data as a spreadsheet.
- View the Working with Lists manual page for more information on creating and managing lists
If you are familiar with the traits on the original version of T3/Oat, you can use the trait lookup table to match the old trait names to their corresponding Breedbase trait names and IDs. There is a trait lookup table available for each crop:
Finish

At this point your Trial(s) and Phenotyping Data have been stored in the database!

The final step is to organize similar Trials together into Folders, which are used to group Trials into Experiments:
1. Go to the Manage > Field Trials page
2. Click the Refresh button above the Trial tree to load the new Trials
3. Click the Create new folder button to create a new folder within a Breeding Program
4. Click the Move trial(s) to folder to add one or more Trial(s) to a folder
5. Click the Refresh button again to display the changes

Complete!

Accessions	Seedlots
Accessions		Breeding Program	Seedlot Name	Contents	Seedlot Location	Count	Weight(g)

Attribute	Value
Project Name:
Start Date:
End Date:
Event Type:
Event Description:
Event Web URL:

Guided Phenotype Upload Workflow

Introduction

Breeding Program(s)

Breeding Program

Locations

Locations

Accessions

Accessions

Trials

Trials

Trait Observations

Phenotype Observations

Finish

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