Phenotype Upload Instructions

These instructions will guide you through the process of creating a phenotype trial and uploading all of its associated data to the database.

If you have any questions about the process, please feel free to Contact Us.

Tutorial

View the notes from a September 2020 workshop on how to load a demo field trial, with step-by-step instructions and example templates, into the database.

Example Templates from the Workshop can be downloaded here:

User Account

In order to submit data to the database, you must have an account with at least submitter privileges. All new accounts created on the sandbox database are automatically given submitter status.

If you need to modify an existing trial, your account must be associated with the breeding program that originally created the trial. If your account is not already associated with the breeding program, please Contact Us to make the change.

  Create Account

Create a new account if you don't already have one


  Login

Login to your existing account

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
  2. If it is not listed, add it to the Database:
 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.

  1. Make sure the Location of your Trial(s) exist in the Database
  2. 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.
  3. 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.
 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
  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.
 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
 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:
    1. Go to the Trial detail page for your trial
    2. Open the Upload Data Files section
    3. 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
    4. After data collection: Click the Upload button next to Android Field Book Exported
    5. 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:
    1. Create a list of Traits that were observed in your trial
    2. Go to the Trial detail page for your trial
    3. Open the Upload Data Files section
    4. 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
    5. Once data has been entered into the template: Click the Upload button next to Phenotyping Spreadsheets to add the recorded observations.
    6. 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:

Submission

Users cannot upload data directly to the production instance of T3/Oat. You can generate the upload templates for each data type and then either:

  • Submit the templates for curation and we will review the files and then submit them to the production database
  • Upload the templates to the Sandbox instance and then submit the individual trials from the sandbox (using the Submit Trial button on the trial detail page of each trial)

Please feel free to Contact Us if you have any questions about data submission.