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BrAPI-Core

BrAPI-Core

The BrAPI-Core module contains high-level entities used for organization and management. This includes Programs, Trials, Studies (Occurrences), Locations, People, and Lists.

GET /programs 22.11

  • Get a filtered list of breeding Programs. This list can be filtered by common crop name to narrow results to a specific crop.

Request (string)

Description GET /programs

CB-DB Reference

Request (string)

Description GET /programs

CB-DB Reference

commonCropName

Filter by the common crop name. Exact match.

tenant.crop.crop_name

programDbId

Program filter to only return trials associated with given program id.

tenant.program.id

programName

Filter by program name. Exact match.

tenant.program.program_name

abbreviation

Filter by program abbreviation. Exact match.

tenant.program.program_code

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

Response Fields

Type

Description GET /programs

CB-DB Reference

Sample Response

Response Fields

Type

Description GET /programs

CB-DB Reference

Sample Response

abbreviation

string

An abbreviation which represents this program

tenant.program.program_code

{ "@context": [ "https://brapi.org/jsonld/context/metadata.jsonld" ], "metadata": { "datafiles": [ { "fileDescription": "This is an Excel data file", "fileMD5Hash": "c2365e900c81a89cf74d83dab60df146", "fileName": "datafile.xlsx", "fileSize": 4398, "fileType": "application/vnd.ms-excel", "fileURL": "https://wiki.brapi.org/examples/datafile.xlsx" } ], "pagination": { "currentPage": 0, "pageSize": 1000, "totalCount": 10, "totalPages": 1 }, "status": [ { "message": "Request accepted, response successful", "messageType": "INFO" } ] }, "result": { "data": [ { "abbreviation": "P1", "additionalInfo": {}, "commonCropName": "Tomatillo", "documentationURL": "https://wiki.brapi.org", "externalReferences": [ { "referenceID": "doi:10.155454/12341234", "referenceSource": "DOI" }, { "referenceID": "http://purl.obolibrary.org/obo/ro.owl", "referenceSource": "OBO Library" }, { "referenceID": "75a50e76", "referenceSource": "Remote Data Collection Upload Tool" } ], "leadPersonDbId": "fe6f5c50", "leadPersonName": "Bob Robertson", "objective": "Make a better tomatillo", "programDbId": "f60f15b2", "programName": "Tomatillo_Breeding_Program" } ] } }

additionalInfo

object

Additional arbitrary info

program metadata? do we have this in EBS?

A: No program metadata

No CB-DB counterpart, return empty

commonCropName

string

Common name for the crop which this program is for

tenant.crop.crop_name
<- tenant.crop_program.crop_id
<- tenant.program.crop_program_id

documentationURL

string
(uri)

A URL to the human-readable documentation of this object

CB Swagger Link (dynamically retrieved depending on the instance used)

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

externalReferences
.referenceID

string

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

No CB-DB counterpart, return null

externalReferences
.referenceSource

string

An identifier for the source system or database of this reference

No CB-DB counterpart, return null

leadPersonDbId

string

The unique identifier of the program leader

No CB-DB counterpart, to be supported in the future sprint, currently stored in CS-DB and CB needs to fetch it

For this sprint, return null

leadPersonName

string

The name of the program leader

No CB-DB counterpart, to be supported in the future sprint, currently stored in CS-DB and CB needs to fetch it

For this sprint, return null

objective

string

The primary objective of the program

tenant.program.description

programDbId*

string

The ID which uniquely identifies the program

tenant.program.id

programName*

string

Human readable name of the program

tenant.program.program_name

GET /studies 22.11

  • Get the list of studies StartDate and endDate should be ISO-8601 format for dates

  • The call returns occurrences which

    • status IN ('planted',add the rest status values here)

    • is_void = FALSE

    • The requester has read or write permissions

Request (string)

Description GET /studies

CB-DB Reference

Request (string)

Description GET /studies

CB-DB Reference

commonCropName

Common name for the crop associated with this trial

tenant.crop.crop_name

studyType

Filter based on study type unique identifier

experiment.experiment_type

programDbId

Program filter to only return studies associated with given program id

tenant.program.program_id

locationDbId

Filter by location

experiment.location.location_id

seasonDbId

Filter by season or year

tenant.season.season_id

trialDbId

Filter by trial

experiment.experiment.experiment_ id

studyDbId

Filter by study DbId

experiment.occurrence.id

studyName

Filter by study name

experiment.occurrence.name

studyCode

Filter by study code

experiment.occurrence.code

studyPUI

Filter by study PUI

No CB-DB counterpart

germplasmDbId

Filter by germplasm DbId Note: Unsupported as of 22.11, need more info on how to map this with the occurrences/studies

germplasm.germplasm.id

observationvariableDbId

Filter by observation variable DbId Note: Unsupported as of 22.11, need more info on how to map this with the occurrences/studies

master.variable.id

sortBy

Name of the field to sort by

Note: We use sort=field:DESC/ASC in cb-api format

sortOrder

Sort order direction. Ascending/Descending

Note: We use sort=field:DESC/ASC in cb-api format

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

Response

Type

Description

CB-DB Reference

Response

Type

Description

CB-DB Reference

active

boolean

Is this study currently active

boolean if occurrence status is planted or mapped

additionalInfo

object

Additional arbitrary info

Possibly occurrence_data, set to empty ({}) for sprint 22.11- need more info if this is required in the Field Book app

commonCropName

string

Common name for the crop associated with this study

tenant.crop.crop_name
<- tenant.crop_program.crop_id
<- tenant.program.crop_program_id
<- experiment.program.program_id

contacts

array[object]

List of contact entities associated with this study

array of contact information

contacts
.contactDbId

string

The ID which uniquely identifies this contact MIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended.

we have steward_id in our experiment.experiment table that could be joined to tenant.person and get the id

contacts
.email

string

The contacts email address MIAPPE V1.1 (DM-32) Person email - The electronic mail address of the person.

we have steward_id in our experiment.experiment table that could be joined to tenant.person and get the email

contacts
.instituteName

string

The name of the institution which this contact is part of MIAPPE V1.1 (DM-35) Person affiliation - The institution the person belongs to

organization_name

contacts
.name

string

The full name of this contact person MIAPPE V1.1 (DM-31) Person name - The name of the person (either full name or as used in scientific publications)

we have steward_id in our experiment.experiment table that could be joined to tenant.person and get the person_name

contacts
.orcid

string

The Open Researcher and Contributor ID for this contact person (http://orcid.org ) MIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended.

No idea, can be blank for now

contacts
.type

string

The type of person this contact represents (ex: Coordinator, Scientist, PI, etc.) MIAPPE V1.1 (DM-34) Person role - Type of contribution of the person to the investigation

No idea, can be blank for now

culturalPractices

string

MIAPPE V1.1 (DM-28) Cultural practices - General description of the cultural practices of the study.

No CB-DB counterpart

dataLinks

array[object]

List of links to extra data files associated with this study. Extra data could include notes, images, and reference data.

array of data link information

dataLinks
.dataFormat

string

The structure of the data within a file. For example - VCF, table, image archive, multispectral image archives in EDAM ontology (used in Galaxy) MIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file.

No idea, can be blank for now

dataLinks
.description

string

The general description of this data link MIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file.

No idea, can be blank for now

dataLinks
.fileFormat

string

The MIME type of the file (ie text/csv, application/excel, application/zip). MIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file.

No idea, can be blank for now

dataLinks
.name

string

The name of the external data link MIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file.

No idea, can be blank for now

dataLinks
.provenance

string

The description of the origin or ownership of this linked data. Could be a formal reference to software, method, or workflow.

No idea, can be blank for now

dataLinks
.scientificType

string

The general type of data. For example- Genotyping, Phenotyping raw data, Phenotyping reduced data, Environmental, etc

No idea, can be blank for now

dataLinks
.url

string
(uri)

URL describing the location of this data file to view or download MIAPPE V1.1 (DM-37) Data file link - Link to the data file (or digital object) in a public database or in a persistent institutional repository; or identifier of the data file when submitted together with the MIAPPE submission.

No idea, can be blank for now

dataLinks
.version

string

The version number for this data MIAPPE V1.1 (DM-39) Data file version - The version of the dataset (the actual data).

No idea, can be blank for now

documentationURL

string
(uri)

A URL to the human readable documentation of this object

CB swagger documentation link

endDate

string
(date-time)

The date the study ends MIAPPE V1.1 (DM-15) End date of study - Date and, if relevant, time when the experiment ended

experiment.location.location_harvest_date (no way to add thru UI right now but can be supported in the future, If users want to set this, they can add harvest_date as occurrence data)

environmentParameters

array[object]

Environmental parameters that were kept constant throughout the study and did not change between observation units. MIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below).

array of env parameters

No CB-DB counterpart, return empty for now

environmentParameters
.description

string

Human-readable value of the environment parameter (defined above) constant within the experiment

 

 

environmentParameters
.parameterName

string

Name of the environment parameter constant within the experiment MIAPPE V1.1 (DM-58) Environment parameter - Name of the environment parameter constant within the experiment.

 

environmentParameters
.parameterPUI

string

URI pointing to an ontology class for the parameter

 

environmentParameters
.unit

string

Unit of the value for this parameter

 

environmentParameters
.unitPUI

string

URI pointing to an ontology class for the unit

 

environmentParameters
.value

string

Numerical or categorical value MIAPPE V1.1 (DM-59) Environment parameter value - Value of the environment parameter (defined above) constant within the experiment.

 

environmentParameters
.valuePUI

string

URI pointing to an ontology class for the parameter value

 

experimentalDesign

object

The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology

list of experiment design info

experimentalDesign.PUI