BrAPI-Phenotyping Concept Dictionary

Events

An event is discrete occurrence at a particular time in the experiment. Events may be the realization of Treatments or parts of Treatments, or may be confounding to Treatments. Can be applied at the whole study level or to only a subset of observation units.

ICASA Management Events allow for the following types: planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other

[also see the MIAPPE definition]

Images

Calls for retrieving, storing, and updating images and image metadata

Implementation Notes:

The Images endpoints support a GeoJSON object structure for describing their location. The BrAPI spec for GeoJSON only supports two of the possible geometries: Points and Polygons.

With most images, the Point geometry should be used, and it should indicate the longitude and latitude of the camera.

For top down images (ie from drones, cranes, etc), the Point geometry may be used to indicate the longitude and latitude of the centroid of the image content, and the Polygon geometry may be used to indicate the border of the image content.

An example use case is available on the BrAPI Wiki -> https://wiki.brapi.org/index.php/Image_Upload

Methods

API to manage the details of observation variable Methods. An observation variable is composed by the unique combination of one Trait, one Method and one Scale. A Method describes the way an observation should be collected. For example, an Observation Variable might be defined with a Trait of “plant height”, a Scale of “meters”, and a Method of “tape measure”. This Variable would be distinct from a Variable with the Method “estimation” or “drone image processing”.

Observation Units

API to retrieve and submit data regarding Observation Units. An Observation Unit is anything that is being observed. Typically, this is a Plot or a Plant, but it could include things like Fields or Samples. The Observation Level defines the type of Observation Unit. For more information on Observation Levels, please review the Observation Levels documentation.

Observation Variables

API to retrieve list and details of observation variables. An observation variable is composed by the unique combination of one Trait, one Method and one Scale.

Observations

API to manage the details of basic phenotypic Observations. An Observation is a value assigned for a specific ObservationVariable when observing a specific ObservationUnit.

Ontologies

API to manage the details of stored Ontologies. This could be a reference a local Ontology or a remote public Ontology.

Scales

API to manage the details of observation variable Scales. An observation variable is composed by the unique combination of one Trait, one Method and one Scale. A Scale describes the units and acceptable values for a Variable. For example, an Observation Variable might be defined with a Trait of “plant height”, a Scale of “meters”, and a Method of “tape measure”. This Variable would be distinct from a Variable with the Scale “inches” or “pixels”.

Traits

API to manage the details of observation variable Traits. An observation variable is composed by the unique combination of one Trait, one Method and one Scale. A Trait describes what property is being observed. For example, an Observation Variable might be defined with a Trait of “plant height”, a Scale of “meters”, and a Method of “tape measure”. This Variable would be distinct from a Variable with the Trait “Leaf length” or “Flower height”.