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Submitting Measured Variables

Submit Measured Variables

Within an experiment various phenotypes can be measured and these are called Measured Variables. Each of these consist of unique triples (three distinct pieces of information) that define:

  • A phenotype
  • How it has been measured
  • Which units have been used

Before the Plots data that contains phenotypic values can be submitted, the required Measured Variables need to have been imported into the system. The form for submitting these ontology terms is available at https://grassroots.tools/private/service/field_trial-submit_measured_variables

The data is submitted as a spreadsheet where each row contains the information for a single Measured Variable and the column headings are described below:

  • Variable Identifier *: This is the unique URI for this variable.
  • Variable Name *: The name of the phenotype being measured. This is the column header that you should use when submitting the Plots data for a Study and it cannot contain any spaces.
  • Variable Description: An optional description of the phenotype being measured.
  • Variable Abbreviation: An optional abbreviation of the phenotype being measured.
  • Trait Identifier *: This is the unique URI for this trait.
  • Trait Name *: The name of the trait being measured.
  • Trait Description: An optional description of the trait being measured.
  • Trait Abbreviation: An optional abbreviation of the trait being measured.
  • Method Identifier *: This is the unique URI for this method.
  • Method Name *: The name of the method used.
  • Method Description: An optional description of the method being used.
  • Method Abbreviation: An optional abbreviation of the method being used.
  • Unit Identifier *: This is the unique URI for this unit.
  • Unit Name *: The name of the unit used.
  • Unit Description: An optional description of the unit being used.
  • Unit Abbreviation: An optional abbreviation of the unit being used.

  • Scale Class *: This denotes that type of values that this Measured Variable can take and we use the possible options defined by the Crop Ontology. These are:

    • Date: The date class is for events expressed in a time format, e.g. “yyyymmdd hh:mm:ss – UTC” or “dd-mm-yy”. A good practice recommended by the Breeding API (BrAPI) is to use the Date and timestamp fields coded in the ISO 8601 standard, extended format. Check the relevant BrAPI docs for more information.
    • Duration: The duration class is for time elapsed between two events expressed in a time format, e.g. “days”, “hours”, “months”.
    • Nominal: Categorical scale that can take one of a limited number of categories. There is no intrinsic ordering to the categories e.g. r=“red”, g=“green”, p=“purple”.
    • Numerical: Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimetre, ton per hectare, number of branches.
    • Ordinal: Ordinal scales are composed of ordered and fixed number of categories e.g. 1=low, 2=moderate, 3=high
    • Text: A free text is used to express the scale value. Also known as Character variable (varchar) e.g. “Preferred when slightly undercooked”.
    • Code: This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example, a disease related code might be expressed by a 2-digit code for intensity and 2-character code for severity. The first 2 digits are the proportion of plants affected by a fungus and the 2 characters refer to the severity, e.g. “75HD” means “75% of the plants are infected and plants are highly damaged”. It is recommended to create variables for every component of the code.

The required attributes are denoted with * and the column headings can be in any order.