Step 1. Create the Program

1. Log into the BreedBase instance as an administrator

2. On the top toolbar, navigate to Manage > Breeding Programs

3. Click "Add New Program". [Large blue button]

4. Enter the program's name and a description. [Both fields of information are required.] [There is a limit of 20 characters for the program name.]

5. Click "Add Breeding Program".

6. Your new program should be added to the list and immediately appear on the page.

Step 2. Load Accessions

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See example file for column headers: AccessionsFileExampleBreedbaseHeader.xls

See example file for filled-in fields: ImportableAccessions.xls

Format the accession file

• These five column headers must be present (and in the following order) in the accession file: accession_name, species_name, population_name, organization_name(s), synonym(s).

• The only columns required to be filled-in with information are accession_name and species_name. However, the file will not upload unless all 5 column headers are present and in the correct order in the uploaded file.

• The file name cannot have any spaces when saved.

• Some versions of BreedBase (prior to mid-2020) will only accept column headers with the (s) appended. Newer versions will accept organization_name and synonym as column headers.

• Check all data carefully for leading and trailing spaces. BreedBase currently does not trim leading and trailing spaces. The system will reject your import with a nondescript system-level warning.

Upload the accession file into BreedBase

1. Within BreedBase, navigate to Manage > Accessions.

2. Click "Add Accession or Upload Accession Info". [It’s in red font in the upper-right corner of the page.]

3. Click "Upload a File".

4. Select the file, then click "Continue". [You can uncheck "Use Fuzzy Search" if you don't want BreedBase to search for similarly named accessions. This will increase the speed of loading accessions into BreedBase.]

Optional Columns

Some users may choose for their accession file to include more column headers than the five that are required for upload. Here are the names of optional column headers and a brief description of each.

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introgression_start_position_bp - The end position of the introgression in base pairs.

Step 3. Load Locations

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See example file for column headers: LocationsFileExampleBreedbaseHeader.xls

See example file for filled-in fields: ImportableLocations.xls

Format the locations file

• These column headers must be present (and in the following order) in the locations file: Name, Abbreviation, Country Code, Country Name, Program, Type, Latitude, Longitude, Altitude, and NOAA Station ID.

• All fields within the required columns must be filled-in according to the following specifications:

Name - Must be unique across the entire database.

Abbreviation - Must be unique across the entire database.

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NOAA Station ID: This is the identifier for the closest NOAA weather station with current data. Visit this web URL: https://www.ncdc.noaa.gov/cdo-web/search . In the field “Enter a Search Term”, type a location name. Choose the ID for the station with current data that is closest to the location of interest. If there is no weather station nearby, you can write ‘none’.

Upload the locations file into BreedBase

1. Within BreedBase, navigate to Manage > Locations.

2. Click "Upload New Locations". [It is in red font, located on the far right.]

3. Click on “Choose File” and select the file, then click "Upload".

Step 4. Load Trials / Experiments

Single trial files may be uploaded into BreedBase one at a time.  Or, you may upload multiple trials and field layouts into BreedBase in one file. 

Uploading a single trial / experiment

See example file with column headers: SingleTrialDesignFileExampleBreedbaseHeader.xls

See example file for filled-in fields: ImportableSingleTrialDesign.xls

Format the single trial / experiment file

• These column headers must be present (and in the following order) in the single trial / experiment file: plot_name, accession_name, plot_number, block_number.

• All fields within the required columns must be filled-in according to the following specifications:

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weight_gram_seed_per_plot – The weight in grams of seeds per plot. Seed is transferred from the seedlot in seedlot name. Must be numeric.

Upload the single trials / experiments file into BreedBase

1. Within BreedBase, navigate to Manage > Field Trials.

2. Click “Upload Existing Trial(s)”. [It is a blue button, located on the right.]

3. Click “Go to Next Step”.

4. “Single Trial Design” should be selected. Click “Go to Next Step.”

5. Enter the following information for the single trial design:
   Trial Name - Must be unique across the entire database. Trial Name is often a concatenation of year, purpose, unique number, and location.

   Breeding_Program - The name of breeding program that managed the trial. Must exist in the database.

   Location - The name of the location where the trial was held. Must exist in the database.

   Trial Type - The name of the trial type. Must exist in the database. Possible values include Seedling Nursery, phenotyping_trial, Advanced Yield Trial, Preliminary Yield Trial, Uniform Yield Trial, Variety Release Trial, Clonal Evaluation, genetic_gain_trial, storage_trial, heterosis_trial, health_status_trial, grafting_trial, Screen House, Seed Multiplication, crossing_block_trial, Specialty Trial.

   Year -The year in which the trial was held.

   Plot Width - Plot width (in meters).

   Plot Length - Plot length (in meters).

   Field Size - Field size (in hectares).

   Description - Additional text with any other relevant information about the trial.

   Stock Type Being Evaluated in Trial – Select from: accession, cross, family_name.

   Design Type – The shorthand for the design type. Must exist in the database. Possible values include Completely Randomized, Complete Block, Alpha Lattice, Lattice, Augmented, Modified Augmented Design, Nursery/Greenhouse, Split Plot, Partially Replicated, and Westcott.

6. Choose the file for upload, then click "Go to Next Step".

7. Click “First validate the form”.

8. Click “Upload”.

9. You should get a message that the trial has been successfully uploaded.

Uploading multiple trials / experiments

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See example file with column headers: MultiLocationMultiTrialExampleBreedbaseHeader.xls. (This file is an expansion of the single trial design header.)

See example file for filled-in fields: ImportableMultiTrialDesign.xls

Format the multiple trials / experiments file

• These column headers must be present (and in the following order) in the trials / experiments file: trial_name, breeding_program, location, year, design_type, description, plot_name, accession_name, plot_number, block_number.

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Treatments - Treatment columns are additional column(s) that specify the name of a treatment (e.g. inoculated, drought, etc). The value for each plot should be 1 if the treatment was applied or empty if not applied.

Upload the multiple trials / experiments file into BreedBase

1. Within BreedBase, navigate to Manage > Field Trials.

2. Click "Upload Existing Trial(s)". [Blue Button on Right side.]

3. You will be guided through the upload process.

   1. Step 1 – Introduction information on what a trial is. Click on “Go to Next Step”

   2. Step 2- Here you will decide to upload a Multi Trial Design. Make sure “Multi Trial Designs” is highlighted in blue. Click “Choose File” and upload the Excel file with trial information.

   3. You should get a message that the trials have been successfully uploaded. 

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