Phenotyping

Specific Treatments

A Specific treatment is an action applying to an environment and characterizing a specific condition in a field trial.

These treatments can be managed in the menu Admin > Phenotyping > Specific treatment.

It is defined by the fields described in the table below. Fields in bold are required while italic ones are optional when submitting the form. Specific treatment can be edited from the table below the form.

Field name	Description
Name	The name of this specific treatment
Description	Description of the treatment. (Nitrogen, water stress etc.)

Environments

An Environment is an object characterizing a field trial in a specific location a given year.

Environments can be managed in the menu Admin > Phenotyping > Environment.

It is defined by the fields described in the table below. Fields in bold are required while italic ones are optional when submitting the form. Environments can be edited from the table below the form.

Field name	Description
Name	The name of this environment
Date	The year of the trial
Location	The site for the experimentation
Description	Description of the environment.
Specific treatment	A specific treatment applied to the trial

Traits

A Trait is a quantifiable phenotypic characteristic.

Traits can be managed in the menu Admin > Phenotyping > Trait.

It is defined by the fields described in the table below. Fields in bold are required while italic ones are optional when submitting the form. Traits can be edited from the table below the form.

Field name	Description
Name	The name of this trait
Abbreviation	Short name used for this trait
Comments	Description of this trait
Ontology_terms	A list of ontology terms (a term must unique in thaliadb ontologies)
Projects	Projects in which the trait is shared

Ontologies

Thaliadb makes possible to describe ontologies commonly used in plant science.

Ontologies can be managed in Admin > Phenotyping > Ontology.

It is defined by the fields described in the table below. Fields in bold are required while italic ones are optional when submitting the form. Ontologies can be edited from the table below the form.

Field name	Description
Ontology_id	The unique id for this ontology (for instance the Maize crop ontology is CO_322)
Name	A name for this ontology
Description	Description of this ontology
URL	A link that points to this ontology
File	The ontology file in Trait Dictionary format

Phenotyping methods

A Phenotypic method is the statistical method used to compute phenotypic values stored in thaliadb.

These type of methods can be managed in the menu Admin > Phenotyping > Statistical method.

It is defined by the fields described in the table below. Fields in bold are required while italic ones are optional when submitting the form. Methods can be edited from the table below the form.

Field name	Description
Name	The name of this phenotypic method
Description	Description of the method
Method file	A file describing or giving information on how the method have been computed

Insert phenotyping data

Phenotyping data can uploaded in Thaliadb with files. The form to submit data files can be found in the menu Admin > Phenotyping > insert data.

The file to submit must be a text CSV format with seedlot in line and traits in column.

Form to upload Phenotypic data