BrAPI-Phenotyping

observationUnitDbId

The unique ID of an Observation Unit

plot_id = experiment.plot.id

germplasmDbId

The unique ID of a germplasm (accession) to filter on

germplasm.germplasm.id

studyDbId

The unique ID of a studies to filter on

experiment.occurrence.id

locationDbId

The unique ID of a location where these observations were collected

experiment.location.id

trialDbId

The unique ID of a trial to filter on

experiment.experiment.id with “Breeding Trial” experiment type

programDbId

The unique ID of a program to filter on

tenant.program.id

seasonDbId

The year or Phenotyping campaign of a multi-annual study (trees, grape, ...)

tenant.season.id

observationUnitLevelName

The Observation Unit Level. Returns only the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelName

plot

observationUnitLevelOrder

The Observation Unit Level Order Number. Returns only the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder

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observationUnitLevelCode

The Observation Unit Level Code. This parameter should be used together with observationUnitLevelName or observationUnitLevelOrder. References ObservationUnit->observationUnitPosition->observationLevel->levelCode

plot.plot_number

includeObservations

Use this parameter to include a list of observations embedded in each ObservationUnit object. CAUTION - Use this parameter at your own risk. It may return large, unpaginated lists of observation data. Only set this value to True if you are sure you need to.

Possible MVI for this sprint: False by default

Note: String type and not a boolen in BrAPI specs

externalReferenceID

An external reference ID. Could be a simple string or a URI. (use with externalReferenceSource parameter)

No CB-DB counterpart

externalReferenceSource

An identifier for the source system or database of an external reference (use with externalReferenceID parameter)

No CB-DB counterpart

additionalInfo

object

Additional arbitrary info

Possibly plot_metadata, set to empty ({}) for sprint 22.11- need more details for the required additional info in the Field Book app

externalReferences

array[object]

An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.

No CB-DB counterpart

string

The external reference ID. Could be a simple string or a URI.

No CB-DB counterpart, return null

string

An identifier for the source system or database of this reference

No CB-DB counterpart, return null

germplasmDbId

string

The ID which uniquely identifies a germplasm

germsplam.germplasm.id

germplasmName

string

Name of the germplasm. It can be the preferred name and does not have to be unique.

germsplam.germplasm.designation

locationDbId

string

The ID which uniquely identifies a location, associated with this study

experiment.location.id

locationName

string

The human readable name of a location associated with this study

experiment.location.name

observationUnitDbId

string

The ID which uniquely identifies an observation unit MIAPPE V1.1 (DM-70) Observation unit ID - Identifier used to identify the observation unit in data files containing the values observed or measured on that unit. Must be locally unique.

plot_id

observationUnitName

string

A human readable name for an observation unit

plot_code

observationUnitPUI

string

A Permanent Unique Identifier for an observation unit MIAPPE V1.1 (DM-72) External ID - Identifier for the observation unit in a persistent repository, comprises the name of the repository and the identifier of the observation unit therein. The EBI Biosamples repository can be used. URI are recommended when possible.

No CB-DB counterpart, return null

observationUnitPosition

object

All positional and layout information related to this Observation Unit MIAPPE V1.1 (DM-73) Spatial distribution - Type and value of a spatial coordinate (georeference or relative) or level of observation (plot 45, subblock 7, block 2) provided as a key-value pair of the form type:value. Levels of observation must be consistent with those listed in the Study section.

list of observation unit position info

string

The type of entry for this observation unit. ex. "CHECK", "TEST", "FILLER"

plot_id → planting_instruction → entry_type

object

One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. Copied from RFC 7946 Section 3.1.1 A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.

geospatial coordinates per plot not yet implemented

No CB-DB counterpart

object

A geometry as defined by GeoJSON (RFC 7946). In this context, only Point or Polygon geometry are allowed.

same comment above

No CB-DB counterpart, return null

string

The literal string "Feature"

same comment above

No CB-DB counterpart, return null

object

The exact level and level code of an observation unit. For more information on Observation Levels, please review the Observation Levels documentation. MIAPPE V1.1 DM-71 Observation unit type "Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. The observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). Alternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead."

plot

string

An ID code for this level tag. Identify this observation unit by each level of the hierarchy where it exists

plot.plot_number

Reference:https://ebsproject.atlassian.net/browse/CORB-6792

string

A name for this level

plot

integer

`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers are at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9).

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array[object]

Observation levels indicate the granularity level at which the measurements are taken. For more information on Observation Levels, please review the Observation Levels documentation. `levelName` defines the level `levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are at the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify this observation unit by each level of the hierarchy where it exists

Currently used by FB new Field Import UI as shared by the PhenoApps team during the hackathon: https://ebsproject.atlassian.net/browse/BDS-6502

• populated same as the observation level 25.10

string

An ID code for this level tag. Identify this observation unit by each level of the hierarchy where it exists

plot.plot_number

string

A name for this level

plot

integer

`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers are at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9).

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observationUnitPosition
.observationLevelRelationships
.observationUnitDbId

string

The ID which uniquely identifies an observation unit
If this level has on ObservationUnit associated with it, record the observationUnitDbId here. This is intended to construct a strict hierarchy of observationUnits.
If there is no ObservationUnit associated with this level, this field can set to NULL or omitted from the response.

plot.id

string

The X position coordinate for an observation unit. Different systems may use different coordinate systems.

Is this in plot level? Yes

plot.field_x → plot.design_x → plot.pa_x

string

The type of positional coordinate used. Must be one of the following values LONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details LATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details PLANTED_ROW - The physical planted row number PLANTED_INDIVIDUAL - The physical counted number, could be independant or within a planted row GRID_ROW - The row index number of a square grid overlay GRID_COL - The column index number of a square grid overlay MEASURED_ROW - The distance in meters from a defined 0-th row MEASURED_COL - The distance in meters from a defined 0-th column

GRID_COL

string

The Y position coordinate for an observation unit. Different systems may use different coordinate systems.

plot.field_y → plot.design_y → plot.pa_y

string

The type of positional coordinate used. Must be one of the following values LONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details LATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details PLANTED_ROW - The physical planted row number PLANTED_INDIVIDUAL - The physical counted number, could be independant or within a planted row GRID_ROW - The row index number of a square grid overlay GRID_COL - The column index number of a square grid overlay MEASURED_ROW - The distance in meters from a defined 0-th row MEASURED_COL - The distance in meters from a defined 0-th column

GRID_ROW

observations

array[object]

All observations attached to this observation unit. Default for this field is null or omitted. Do NOT include data in this field unless the 'includeObservations' flag is explicitly set to True.

All plot_data records linked via plot_id

object

Additional arbitrary info

plot_data metadata like remarks?

For now, set to empty {}

string

The name or identifier of the entity which collected the observation

collector_id or creator_id for now

array[object]

An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.

No CB-DB counterpart

string

The external reference ID. Could be a simple string or a URI.

No CB-DB counterpart, return null

string

An identifier for the source system or database of this reference

No CB-DB counterpart, return null

string

The ID which uniquely identifies a germplasm

germplasm.germplasm.id

string

Name of the germplasm. It can be the preferred name and does not have to be unique.

germplasm.germplasm.name

string

The ID which uniquely identifies an observation

plot_data.id

string
(date-time)

The date and time when this observation was made

plot_data.collection_timestamp

string

The ID which uniquely identifies an observation unit

plot_id

string

A human-readable name for an observation unit

plot_code

string

The ID which uniquely identifies an observation variable

master.variable.id

string

A human-readable name for an observation variable

master.variable.name

object

list of observation season info

string

Name of the season. ex. 'Spring', 'Q2', 'Season A', etc.

tenant.season.season_name

string

The ID which uniquely identifies a season. For backward compatibility it can be a string like '2012', '1957-2004'

tenant.season.id

integer

The 4-digit year of the season.

traverse up to experiment_year

string

The ID which uniquely identifies a study within the given database server

experiment.occurrence.id

string

The name or id of the user who uploaded the observation to the database system

plot_data.creator_id