Guided Phenotype Upload Workflow



  1. Intro
  2. Breeding Program
  3. Locations
  4. Accessions
  5. Trials
  6. Observations
  7. Finish

  1. Introduction

    This workflow will guide your through the basic steps required for adding one or more phenotyping / field trials to the database:



    Download Templates  


  2. 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:

    NameDescription


    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  


  3. 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:

    NameAbbreviationCountryTrials


    If your Location(s) exist:

    Continue to the next step


    If your Location(s) do not exist:

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


    Detailed Instructions  


  4. 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:



    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  


  5. 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:

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


    Detailed Instructions  


  6. 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  


  7. 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!
Complete!


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89711dec3   sgn-358.0
Fri Jul 21 07:51:15 2023 -0400

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T3 is part of the Wheat CAP project, supported by Agriculture and Food Research Initiative Competitive Grant no. 2011-68002-30029 from the USDA National Institute of Food and Agriculture.