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Phenotyping Module

Observation Units

GET /observationunits

Supported Parameters

Data Type Parameter Name Description
integer page Used to request a specific page of data to be returned. The page indexing starts at 0 (the first page is 'page'= 0). Default is 0.
integer pageSize The size of the pages to be returned. Default is 1000.
string germplasmDbId Use this parameter to only return results associated with the given Germplasm unique identifier. Use GET /germplasm to find the list of available Germplasm on a server.

Example Response

Response Code 200
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{
  "metadata": {
    "pagination": {
      "currentPage": 0,
      "pageSize": 1,
      "totalCount": 996,
      "totalPages": null
    },
    "status": [
      {
        "message": "Success",
        "messageType": "INFO"
      }
    ],
    "datafiles": []
  },
  "result": {
    "data": [
      {
        "additionalInfo": null,
        "crossDbId": null,
        "crossName": null,
        "externalReferences": null,
        "germplasmDbId": "HOR 4402",
        "germplasmName": "HOR 4402",
        "locationDbId": null,
        "locationName": null,
        "observationUnitDbId": "HOR 4402_1105630",
        "observationUnitName": "HOR 4402_1105630",
        "observationUnitPUI": null,
        "observationUnitPosition": null,
        "observations": null,
        "programDbId": null,
        "programName": null,
        "seedLotDbId": null,
        "seedLotName": null,
        "studyDbId": "Barley Spike Investigation",
        "studyName": "Barley Spike Investigation",
        "treatments": null,
        "trialDbId": "bridge",
        "trialName": "BRIDGE core1000"
      }
    ]
  }
}

GET /observationunits/{observationUnitDbId}

Supported Parameters

Data Type Parameter Name Description
string trialDbId The internal trial identifier.

Example Response

Response Code 200
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{
  "metadata": {
    "pagination": {
      "currentPage": 0,
      "pageSize": 1,
      "totalCount": 1,
      "totalPages": 1
    },
    "status": [
      {
        "message": "Success",
        "messageType": "INFO"
      }
    ],
    "datafiles": []
  },
  "result": {
    "additionalInfo": null,
    "crossDbId": null,
    "crossName": null,
    "externalReferences": null,
    "germplasmDbId": "HOR 4402",
    "germplasmName": "HOR 4402",
    "locationDbId": null,
    "locationName": null,
    "observationUnitDbId": "HOR 4402_1105630",
    "observationUnitName": "HOR 4402_1105630",
    "observationUnitPUI": null,
    "observationUnitPosition": null,
    "observations": null,
    "programDbId": null,
    "programName": null,
    "seedLotDbId": null,
    "seedLotName": null,
    "studyDbId": "Barley Spike Investigation",
    "studyName": "Barley Spike Investigation",
    "treatments": null,
    "trialDbId": "bridge",
    "trialName": "BRIDGE core1000"
  }
}

Observation Variables

GET /variables

Supported Parameters

Data Type Parameter Name Description
integer page Used to request a specific page of data to be returned. The page indexing starts at 0 (the first page is 'page'= 0). Default is 0.
integer pageSize The size of the pages to be returned. Default is 1000.
string observationVariableDbId Variable's unique ID

Example Response

Response Code 200
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{
  "metadata": {
    "pagination": {
      "currentPage": 0,
      "pageSize": 1,
      "totalCount": 15,
      "totalPages": 15
    },
    "status": [
      {
        "message": "Success",
        "messageType": "INFO"
      }
    ],
    "datafiles": []
  },
  "result": {
    "data": [
      {
        "additionalInfo": null,
        "commonCropName": null,
        "contextOfUse": null,
        "defaultValue": null,
        "documentationURL": null,
        "externalReferences": null,
        "growthStage": null,
        "institution": null,
        "language": null,
        "method": {
          "additionalInfo": null,
          "bibliographicalReference": null,
          "description": null,
          "externalReferences": null,
          "formula": null,
          "methodClass": null,
          "methodDbId": "Row-Type Estimation",
          "methodName": null,
          "methodPUI": null,
          "ontologyReference": null
        },
        "observationVariableDbId": "CONVAR",
        "observationVariableName": "Row-Type convarity",
        "observationVariablePUI": null,
        "ontologyReference": null,
        "scale": {
          "additionalInfo": null,
          "dataType": "Nominal",
          "decimalPlaces": null,
          "externalReferences": null,
          "ontologyReference": null,
          "scaleDbId": "1to5RowType",
          "scaleName": null,
          "scalePUI": null,
          "units": null,
          "validValues": {
            "categories": [
              {
                "label": "'convar. distichon'",
                "value": "1"
              },
              {
                "label": "'convar. deficiens'",
                "value": "2"
              },
              {
                "label": "'convar. labile'",
                "value": "3"
              },
              {
                "label": "'convar. intermedium'",
                "value": "4"
              },
              {
                "label": "'convar. vulgare/convar. hexastichon'",
                "value": "5"
              }
            ],
            "maximumValue": null,
            "minimumValue": null
          }
        },
        "scientist": null,
        "status": null,
        "submissionTimestamp": null,
        "synonyms": null,
        "trait": {
          "additionalInfo": null,
          "alternativeAbbreviations": null,
          "attribute": null,
          "attributePUI": null,
          "entity": null,
          "entityPUI": null,
          "externalReferences": null,
          "mainAbbreviation": null,
          "ontologyReference": null,
          "status": null,
          "synonyms": null,
          "traitClass": "morphological",
          "traitDbId": "Row-Type convarity",
          "traitDescription": null,
          "traitName": null,
          "traitPUI": null
        }
      }
    ]
  }
}

GET /variables/{observationVariableDbId}

Supported Parameters

Data Type Parameter Name Description
string trialDbId The internal trial identifier.

Example Response

Response Code 200
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{
  "metadata": {
    "pagination": {
      "currentPage": 0,
      "pageSize": 0,
      "totalCount": 1,
      "totalPages": 1
    },
    "status": [
      {
        "message": "Success",
        "messageType": "INFO"
      }
    ],
    "datafiles": []
  },
  "result": {
    "additionalInfo": null,
    "commonCropName": null,
    "contextOfUse": null,
    "defaultValue": null,
    "documentationURL": null,
    "externalReferences": null,
    "growthStage": null,
    "institution": null,
    "language": null,
    "method": {
      "additionalInfo": null,
      "bibliographicalReference": null,
      "description": null,
      "externalReferences": null,
      "formula": null,
      "methodClass": null,
      "methodDbId": "Row-Type Estimation",
      "methodName": null,
      "methodPUI": null,
      "ontologyReference": null
    },
    "observationVariableDbId": "CONVAR",
    "observationVariableName": "Row-Type convarity",
    "observationVariablePUI": null,
    "ontologyReference": null,
    "scale": {
      "additionalInfo": null,
      "dataType": "Nominal",
      "decimalPlaces": null,
      "externalReferences": null,
      "ontologyReference": null,
      "scaleDbId": "1to5RowType",
      "scaleName": null,
      "scalePUI": null,
      "units": null,
      "validValues": {
        "categories": [
          {
            "label": "'convar. distichon'",
            "value": "1"
          },
          {
            "label": "'convar. deficiens'",
            "value": "2"
          },
          {
            "label": "'convar. labile'",
            "value": "3"
          },
          {
            "label": "'convar. intermedium'",
            "value": "4"
          },
          {
            "label": "'convar. vulgare/convar. hexastichon'",
            "value": "5"
          }
        ],
        "maximumValue": null,
        "minimumValue": null
      }
    },
    "scientist": null,
    "status": null,
    "submissionTimestamp": null,
    "synonyms": null,
    "trait": {
      "additionalInfo": null,
      "alternativeAbbreviations": null,
      "attribute": null,
      "attributePUI": null,
      "entity": null,
      "entityPUI": null,
      "externalReferences": null,
      "mainAbbreviation": null,
      "ontologyReference": null,
      "status": null,
      "synonyms": null,
      "traitClass": "morphological",
      "traitDbId": "Row-Type convarity",
      "traitDescription": null,
      "traitName": null,
      "traitPUI": null
    }
  }
}

Observations

GET /observations

Supported Parameters

Data Type Parameter Name Description
integer page Used to request a specific page of data to be returned. The page indexing starts at 0 (the first page is 'page'= 0). Default is 0.
integer pageSize The size of the pages to be returned. Default is 1000.
string studyDbId Use this parameter to only return results associated with the given Study unique identifier. Use GET /studies to find the list of available Studies on a server.
string germplasmDbId Use this parameter to only return results associated with the given Germplasm unique identifier. Use GET /germplasm to find the list of available Germplasm on a server.
string observationUnitDbId The unique ID of an Observation Unit
string observationVariableDbId The unique ID of an observation variable

Example Response

Response Code 200
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{
  "metadata": {
    "pagination": {
      "currentPage": 0,
      "pageSize": 1,
      "totalCount": 14925,
      "totalPages": 14925
    },
    "status": [
      {
        "message": "Success",
        "messageType": "INFO"
      }
    ],
    "datafiles": []
  },
  "result": {
    "data": [
      {
        "additionalInfo": null,
        "collector": null,
        "externalReferences": null,
        "geoCoordinates": null,
        "germplasmDbId": "HOR 4402",
        "germplasmName": "HOR 4402",
        "observationDbId": "HOR 4402_1105630-SPIKE_LENGTH-Tue Sep 20 00:00:00 UTC 2016",
        "observationTimeStamp": "2016-09-20T00:00:00+00:00",
        "observationUnitDbId": "HOR 4402_1105630",
        "observationUnitName": null,
        "observationVariableDbId": "SPIKE_LENGTH",
        "observationVariableName": "Spike length",
        "season": null,
        "studyDbId": "Barley Spike Investigation",
        "studyName": "Barley Spike Investigation",
        "uploadedBy": null,
        "value": "9.0"
      }
    ]
  }
}

GET /observations/{observationDbId}

Supported Parameters

Data Type Parameter Name Description
string trialDbId The internal trial identifier.

Example Response

Response Code 200
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{
  "metadata": {
    "pagination": {
      "currentPage": 0,
      "pageSize": 1,
      "totalCount": 1,
      "totalPages": 1
    },
    "status": [
      {
        "message": "Success",
        "messageType": "INFO"
      }
    ],
    "datafiles": []
  },
  "result": {
    "additionalInfo": null,
    "collector": null,
    "externalReferences": null,
    "geoCoordinates": null,
    "germplasmDbId": null,
    "germplasmName": null,
    "observationDbId": "HOR 4402_1105630-SPIKE_LENGTH-Tue Sep 20 00:00:00 UTC 2016",
    "observationTimeStamp": "2016-09-20T00:00:00+00:00",
    "observationUnitDbId": "HOR 4402_1105630",
    "observationUnitName": null,
    "observationVariableDbId": "SPIKE_LENGTH",
    "observationVariableName": null,
    "season": null,
    "studyDbId": null,
    "studyName": null,
    "uploadedBy": null,
    "value": "9.0"
  }
}

GET /observations/table

Supported Parameters

Data Type Parameter Name Description
integer page Used to request a specific page of data to be returned. The page indexing starts at 0 (the first page is 'page'= 0). Default is 0.
integer pageSize The size of the pages to be returned. Default is 1000.
string studyDbId Use this parameter to only return results associated with the given Study unique identifier. Use GET /studies to find the list of available Studies on a server.

Example Response

Response Code 200
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{
  "metadata": {
    "pagination": {
      "currentPage": 0,
      "pageSize": 1,
      "totalCount": 15,
      "totalPages": 15
    },
    "status": [
      {
        "message": "Success",
        "messageType": "INFO"
      }
    ],
    "datafiles": []
  },
  "result": {
    "data": [
      [
        "HOR 4402_1105630",
        "2016-09-20T00:00:00+00:00",
        "9.0",
        "1.0",
        "1.0",
        "3.0",
        "3.0",
        "2.0",
        "1.0",
        "18.5",
        "2.0",
        "1.0",
        "1.0",
        "5.0",
        "1.0",
        "None",
        "3.0"
      ]
    ],
    "headerRow": [
      "observationUnitDbId",
      "observationTimeStamp"
    ],
    "observationVariables": [
      {
        "observationVariableDbId": "SPIKE_LENGTH",
        "observationVariableName": "Spike length"
      },
      {
        "observationVariableDbId": "RACHILLA_HAIRS",
        "observationVariableName": "Rachilla hairs"
      },
      {
        "observationVariableDbId": "GLUME_COLOR",
        "observationVariableName": "Color of glumes"
      },
      {
        "observationVariableDbId": "AWNS_LATERAL",
        "observationVariableName": "Awns lateral spikelets"
      },
      {
        "observationVariableDbId": "SPIKE_DENSITY",
        "observationVariableName": "Spike density"
      },
      {
        "observationVariableDbId": "SPIKE_BRITTLENESS",
        "observationVariableName": "Spike brittleness"
      },
      {
        "observationVariableDbId": "AWNS_GLUMES",
        "observationVariableName": "Awns on glumes"
      },
      {
        "observationVariableDbId": "AWNS_LENGTH",
        "observationVariableName": "Awns length "
      },
      {
        "observationVariableDbId": "AWNS_ROUGHNESS",
        "observationVariableName": "Awns roughness"
      },
      {
        "observationVariableDbId": "GRAIN_HULL",
        "observationVariableName": "Grain hull / Cover of caryopses"
      },
      {
        "observationVariableDbId": "SPIKE_BRANCHING",
        "observationVariableName": "Spike branching"
      },
      {
        "observationVariableDbId": "CONVAR",
        "observationVariableName": "Row-Type convarity"
      },
      {
        "observationVariableDbId": "WIDTH_GLUMES",
        "observationVariableName": "Glume width"
      },
      {
        "observationVariableDbId": "GRAIN_COLOR",
        "observationVariableName": "Color of naked seeds"
      },
      {
        "observationVariableDbId": "AWNS_CENTRAL",
        "observationVariableName": "Awns central spikelets"
      }
    ]
  }
}