Uploading Trials into BreedBase via BreedBase

 

These instructions provide the minimum steps needed to create a field trial or experiment in BreedBase.

  • Right-click to open the hyperlinks in these instructions as new tabs.

  • All files must be uploaded into BreedBase as Excel files (.xls) The .xlsx format is not supported.

  • To save a file as an Excel file (.xls), use ‘save as type’ and select Excel 97-2003 Workbook in Excel.

Step 1. Create the Program

About Breeding Programs. All data (such as Accessions and Trials) in BreedBase are associated with a particular Breeding Program. Generally, we have a Breeding Program for each university or institution that submits data to the database.

The program name will become the highest level for organizing your experiments and trials. All trials and experiments will be listed under the program name you set.

  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

About 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.

All accessions can be uploaded in one file. Accession names must all be unique.

If you created your master list of accession names by copying and pasting from multiple trials, be sure to remove accession names that are duplicated between trials.

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.

population_name - A population is a grouping of accessions. If the population already exists in the database, the accession will be added into it. Otherwise, the new population will be created.

organization_name(s) - The name(s) of the organization(s) that use this accession. If multiple organizations are given, each organization name should be separated by a comma (e.g. NARO,IITA).

synonym(s) - An accession can be known by many names, including local popular names. A synonym name can be used instead of the accession_name throughout the database; therefore, synonyms must themselves be unique. If multiple synonyms are given, each synonym should be separated by a comma (e.g. accession_synonym1,accession_synonym001).

location_code(s) - Location code(s) for the accession. Many can be uploaded at once using a comma-separated list.

ploidy_level(s) - A number indicating the ploidy (e.g. 2 for diploid, 3 for triploid). Many values can be uploaded at once as a comma-separated list.

genome_structure(s) – The genome structure(s) for the accession, which takes ploidy and ancestral genome information (e.g. AAA, AB) into account. Many can be uploaded at once as a comma-separated list.

variety(s) - Variety can be defined as a group of individuals or plants having similar traits that can be reproduced "true to type" from generation to generation. Many can be uploaded at once as a comma-separated list.

donor(s) - The accession_name of the donor accession. Many can be uploaded at once as a comma-separated list.

donor_institute(s) - The institute of the donor accession. Many can be uploaded at once as a comma-separated list.

donor_PUI(s) - The permanent unique identifier of the donor accession. Many can be uploaded at once as a comma-separated list.

country_of_origin(s) - The country of origin for the accesssion. Many can be uploaded at once as a comma-separated list.

state(s) - The state of origin for the accession. Many can be uploaded at once as a comma-separated list.

institute_code(s) - The institute code of origin for the accession. Many can be uploaded at once as a comma-separated list.

institute_name(s) - The institute name of origin for the accession. Many can be uploaded at once as a comma-separated list.

biological_status_of_accession_code(s) – A code indicating the biological status of the accession. Many can be uploaded at once as a comma-separated list.

Notes(s) - Free text for notes. Many notes can be uploaded at once as a comma-separated list.

accession_number(s) -The accession number for accessions from a germplasm bank. Many can be uploaded at once as a comma-separated list.

PUI(s) -The permanent unique identifier of the accession. Many can be uploaded at once as a comma-separated list.

seed_source(s) – The origin of the seed source. Many can be uploaded at once as a comma-separated list.

type_of_germplasm_storage_code(s) – A code indicating the type of germplasm storage. Many can be uploaded at once as a comma-separated list.

acquisition_date(s) -The date(s) of acquisition of the accession in the format YYYYMMDD. Many can be uploaded at once as a comma-separated list.

transgenic - Indicates if the accession is transgenic. Please indicate 1 if transgenic and empty if otherwise.

introgression_parent - If the accession has an introgression that originated from one of the parents, you can specify the parent here.

introgression_backcross_parent – The backcrossed parent for introducing an introgression into the accession.

introgression_map_version - The map version for identifying the start and stop position of the introgression (e.g. AGPv2).

introgression_chromosome - The number of the chromosome on which the introgression occurs.

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

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

Step 3. Load Locations

All locations can be uploaded in one file.

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.

Country Code - Must be an ISO Alpha-3 country code. See https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3 .  For locations in the United States, enter “USA”.)

Country Name - Must be an uppercase English short name from the ISO standard. See https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3 . (For locations in the United States, enter “United States”.

Program - Must be an existing Breeding Program in the database, or multiple breeding programs separated by '&' (e.g. Daisy&Mandrake).

Type: Must be one of the following: Farm, Field, Greenhouse, Screenhouse, Lab, Storage, Other.

Latitude: (in degrees) Must be a number between 90 and -90.

Longitude: (in degrees) Must be a number between 180 and -180.

Altitude: (in meters) Must be a number between -418 (Dead Sea) and 8,848 (Mt. Everest).

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:

plot_name - Must be unique across the entire database. The plot name is often a concatenation of the trial name and the plot number.

accession_name - The accession being tested in the plot. Must exist in the database.

plot_number - A sequential number for the plot in the field (e.g. 1001, 1002, 2001, 2002). These numbers should be unique for the trial.

block_number - A design parameter indicating which block the plot is in.

  • Users may choose for trial / experiment files to include more column headers than the four that are required for upload. Here are the names of optional column headers for trials / experiments and a brief description of each.

is_a_control – Enter a value of 1 into this form field if the plot is a control. Otherwise, enter 0 or leave the form field blank.

rep_number - Replicate number. Must be numeric.

range_number -Often synonymous with col_number. Must be numeric.

row_number - If the field is a grid, row_number represents the y-coordinate. Required for field map generation. Must be numeric.

col_number – Sometimes called range_number. If the field is a grid, col_number represents the x-coordinate. Required for field map generation. Must be numeric.

seedlot_name - The seedlot from which the planted seed originated. Must exist in the database.

num_seed_per_plot – The number of seeds per plot. Seed is transferred from the seedlot in seedlot_name. Must be numeric.

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

Multiple trials can be uploaded into BreedBase via a single document. The trials can be multiple trials in a single location or trials across multiple locations.

The multi-location trial file requires much more information be filled in before it is uploaded compared to the single trial upload file.

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.

(For single trial upload, much of the following required column header information was filled-in via the questionnaire. However, for multiple trial / experiments upload, the information must be provided in the Excel file.)

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

trial_name - Must be unique across entire database. It is often a concatenation of the 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.

year - The year the trial was held.

design_type - The shorthand for the design type. Must exist in the database. Possible values include CRD (Completely Randomized Design), RCBD (Randomized Complete Block Design), Alpha (Alpha Lattice Design), Lattice ( Lattice Design), Augmented (Augmented Design), MAD (Modified Augmented Design), Greenhouse (Greenhouse layour/design), p-rep (Partially replicated design), splitplot (splitplot design), Westcott (Westcott Design).

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

plot_name - Must be unique across entire database. It is often a concatenation of the trial name and the plot number.

accession_name - The accession being tested in the plot. Must exist in the database.

plot_number - A sequential number for the plot in the field (e.g. 1001, 1002, 2001, 2002). These numbers should be unique for the trial.

block_number - A design parameter indicating which block the plot is in.

  • Users may choose for trial / experiment files to include more column headers than the ten that are required for upload. Here are the names of optional column headers for trials / experiments and a brief description of each.

(If additional column headers are included, leave optional column information blank rather than writing “NA”.)

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.

plot_width - Plot width (in meters).

plot_length - Plot length (in meters).

field_size - Field size (in hectares).

planting_date - Date of Planting in YYYY-MM-DD format

harvest_date - Date of Harvest in YYYY-MM-DD format

is_a_control – Enter a value of 1 into this form field if the plot is a control. Otherwise, enter 0 or leave the form field blank.

rep_number - Replicate number. Must be numeric.

range_number - Often synonymous with col_number. Must be numeric.

row_number - If the field is a grid, row_number represents the y-coordinate. Required for field map generation. Must be numeric.

col_number – Sometimes called range_number. If the field is a grid, col_number represents the x-coordinate. Required for field map generation. Must be numeric.

seedlot_name - The seedlot from which the planted seed originated. Must exist in the database.

num_seed_per_plot – The number of seeds per plot. Seed is transferred from the seedlot in seedlot_name. Must be numeric.

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.

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.