Observation (Labs)

Laboratory data are mapped to FHIR's Observation resource. Data are ingested into the Clinical Research Data Warehouse via HL7 message from MSK's Laboratory Information System (LIS) and mapped to a trial visit by clinical research staff.

NOTE: If available in the source data, a LOINC code is mapped to code.coding.code, otherwise the code.coding.code does not appear in the response. Please refer to the protocol specific Data Transfer Specification for a list of test names and LOINC codes relevant to your study.

For guidance on mapping LOINC codes to CDISC or for additional test information, such as the analyte measured or specimen type upon which the observation was made, check out LOINC's FHIR terminology service.

Request

GET /msk-apim/external/v2/crit/blaze/api/observation
-H Authorization: Bearer {access_token} 
-H x-partnerid: {partnerId}

Query Parameters

Parameters	Type	Is Required	Description
category	string	true	For lab data use laboratory
researchstudy	string	true	MSK unique study number
x-partnerid	string	true	MSK provided partner ID

For a list of optional filtering parameters visit the Searching page.

Example Code

C# Python

var client = new RestClient("BASE_URL_PLUS_API_PATH?category={A2}&researchstudy={A1}");
client.Timeout = -1;
var request = new RestRequest(Method.GET);
request.AddHeader("Authorization", "Bearer {ACCESS_TOKEN}");
request.AddHeader("x-partnerid", "{partnerId}");
IRestResponse response = client.Execute(request);
Console.WriteLine(response.Content);

import http.client

conn = http.client.HTTPSConnection("BASE_URL")
payload = ''
headers = {
'Authorization': 'Bearer {ACCESS_TOKEN}',
'x-partnerid': '{partnerId}'
}
conn.request("GET", "API_PATH?category={A2}&researchstudy={A1}", payload, headers)
res = conn.getresponse()
data = res.read()
print(data.decode("utf-8"))

Response

Successful Payload Example

  {
    "resourceType": "Bundle",
    "identifier": {
        "system": "https://fhir.mskcc.org/structure-definitions/#IDB.Protocol",
        "value": "FHIR-T"
    },
    "type": "searchset",
    "total": 103,
    "link": [
        {
          "relation": "self",
          "url": "https://apigateway.apps.stageapi.mskcc.org/msk-apim/external/v2/crit/blaze/api/Observation?category=laboratory&researchstudy=FHIR-T&page=1"
        },
        {
          "relation": "first",
          "url": "https://apigateway.apps.stageapi.mskcc.org/msk-apim/external/v2/crit/blaze/api/Observation?category=laboratory&researchstudy=FHIR-T&page=1"
        },
        {
          "relation": "last",
          "url": "https://apigateway.apps.stageapi.mskcc.org/msk-apim/external/v2/crit/blaze/api/Observation?category=laboratory&researchstudy=FHIR-T&page=3"
        },
        {
          "relation": "next",
          "url": "https://apigateway.apps.stageapi.mskcc.org/msk-apim/external/v2/crit/blaze/api/Observation?category=laboratory&researchstudy=FHIR-T&page=2"
        }
        ],
"entry": [
    {
            "fullUrl": "https://apigateway.apps.stageapi.mskcc.org/msk-apim/external/v2/crit/blaze/api/Observation?category=laboratory&researchstudy=FHIR-T&_Id=500009866",
            "resource": {
            "resourceType": "Observation",
            "id": "500009866",
            "extension": [
              {
                "url": "https://fhir.mskcc.org/structure-definitions/#IDB.Protocol",
                "valueString": "FHIR-T"
              },
              {
                "url": "https://fhir.mskcc.org/structure-definitions/#SponsorID",
                "valueString": "C3861001"
              }
            ],
            "identifier": [
              {
                "system": "https://fhir.mskcc.org/structure-definitions/#LAB_RESULTS.LR_RESULT_GUID",
                "value": "500009866"
              }
            ],
            "status": "final",
            "category": [
              {
                "coding": [
                  {
                    "system": "http://hl7.org/fhir/2021Mar/valueset-observation-category.html",
                    "code": "laboratory",
                    "display": "Laboratory"
                  }
                ],
                "text": "Laboratory"
              }
            ],
            "code": {
              "coding": [
                {
                  "system": "https://loinc.org",
                  "code": "704-7",
                  "display": "ABAS"
                }
              ],
              "text": "ABAS"
            },
            "subject": {
              "reference": "Patient/10081007"
            },
            "encounter": {
              "display": "CYCLE1_DAY1"
            },
            "effectiveDateTime": "2021-12-14T02:03:00",
            "issued": "2022-02-15T09:47:08+05:30",
            "performer": [
              {
                "display": "Practitioner/YAN"
              }
            ],
            "valueQuantity": {
              "value": 0,
              "unit": "K/mcL"
            },
            "referenceRange": [
              {
                "text": "0.0-0.2"
              }
          ]
       }
    },
    {
        "fullUrl": "https://apigateway.apps.stageapi.mskcc.org/msk-apim/external/v2/crit/blaze/api/Observation?category=laboratory&researchstudy=FHIR-T&_Id=500009867",
        "resource": {
        "resourceType": "Observation",
        "id": "500009867",
        "extension": [
            {
            "url": "https://fhir.mskcc.org/structure-definitions/#IDB.Protocol",
            "valueString": "FHIR-T"
            },
            {
            "url": "https://fhir.mskcc.org/structure-definitions/#SponsorID",
            "valueString": "C3861001"
            }
        ],
        "identifier": [
            {
            "system": "https://fhir.mskcc.org/structure-definitions/#LAB_RESULTS.LR_RESULT_GUID",
            "value": "500009867"
            }
        ],
        "status": "final",
        "category": [
            {
            "coding": [
                {
                "system": "http://hl7.org/fhir/2021Mar/valueset-observation-category.html",
                "code": "laboratory",
                "display": "Laboratory"
                }
            ],
            "text": "Laboratory"
            }
        ],
        "code": {
            "coding": [
            {
                "system": "https://loinc.org",
                "code": "711-2",
                "display": "AEOS"
            }
            ],
            "text": "AEOS"
        },
        "subject": {
            "reference": "Patient/10081007"
        },
        "encounter": {
            "display": "CYCLE1_DAY1"
        },
        "effectiveDateTime": "2021-12-14T02:03:00",
        "issued": "2022-02-15T09:47:08+05:30",
        "performer": [
            {
            "display": "Practitioner/YAN"
            }
        ],
        "valueQuantity": {
            "value": 0.3,
            "unit": "K/mcL"
        },
        "referenceRange": [
            {
            "text": "0.0-0.7"
            }
        ]
      }
    }
  ]
}

Field Definitions

Field	Description
id	MSK Unique Identifier
extension[0].url	FHIR Structure Definition documentation
extension[0].valueCode	MSK IRB Protocol Number
extension[1].url	FHIR Structure Definition documentation
extension[1].valueCode	Sponsor Study Number
identifier.system	FHIR Structure Definition documentation
identifier.value	MSK Unique Identifier
status	Hardcoded to final
category.coding.system	FHIR Observation category documentation
category.coding.code	FHIR Observation category code
category.coding.display	FHIR Observation category display
category.text	FHIR Observation category
code.coding.system	LOINC documentation
code.coding.code	LOINC code
code.coding.display	MSK test code
code.text	MSK test code
subject.reference	Patient/ + Sponsor assigned subject ID
effectiveDateTime	Specimen collection datetime
issued	Specimen datetime
valueQuantity.value	Numeric result
valueQuantity.unit	Test Unit
valueString	Text result
referenceRange.text	Reference range
encounter.display	Protocol visit
performer.display	Practitioner/ + Practitioner (CRT) ID