DEQ

Schema and example JSON files describing the Data Extraction Query (DEQ) for the FDPG+ framework used to extract medical data based on specific criteria defined in a cohort. The query provides a what data to extract from a defined cohort.

Purpose

The DEQ is utilized to describe data extraction inside the FDPG+ infrastructure. TBD:more desc.

Structure

A DEQ consists of 2 Parts: The cohort definition in CCDL, see CCDL specs for further details and a data extraction object.

The data extraction object contains an array defining attributeGroups, which bundle attributes together.

Each group has an identifier for the group called groupReference, a list of attributes to be extracted attributes and list of filters filters.

An attributes to be extracted contains an attribute reference attributeRef and information if the attribute is required must-have e.g. { "attributeRef": "medicationCode", "mustHave": true }.

If a must have condition is violated, it will result in a complete stop of the extraction for a patient.

Filters definition is equivalent to the filter definition in CCDL.

Example

Here is a example of a DEQ JSON:

{
  "version": "http://to_be_decided.com/draft-1/schema#",
  "display": "Data Extraction for Cardiovascular Study",
  "cohortDefinition": {
    "version": "http://to_be_decided.com/draft-1/schema#",
    "display": "Cardiovascular Disease Patients 18+",
    "inclusionCriteria": [
      [
        {
          "termCodes": [
            {
              "code": "424144002",
              "system": "http://snomed.info/sct",
              "display": "Current chronological age"
            }
          ],
          "context": {
            "code": "Patient",
            "system": "fdpg.mii.cds",
            "version": "1.0.0",
            "display": "Patient"
          },
          "valueFilter": {
            "type": "quantity-comparator",
            "unit": {
              "code": "a",
              "display": "years"
            },
            "value": 18,
            "comparator": "gt"
          }
        }
      ],
      [
        {
          "termCodes": [
            {
              "code": "53741008",
              "system": "http://snomed.info/sct",
              "display": "Coronary artery disease"
            }
          ],
          "context": {
            "code": "Diagnosis",
            "system": "fdpg.mii.cds",
            "version": "1.0.0",
            "display": "Diagnosis"
          }
        }
      ]
    ],
    "exclusionCriteria": [
      [
        {
          "termCodes": [
            {
              "code": "38341003",
              "system": "http://snomed.info/sct",
              "display": "Hypertension"
            }
          ],
          "context": {
            "code": "Condition",
            "system": "fdpg.mii.cds",
            "version": "1.0.0",
            "display": "Condition"
          }
        }
      ]
    ]
  },
  "dataExtraction": {
    "attributeGroups": [
      {
        "groupReference": "MedicationDetails",
        "attributes": [
          {
            "attributeRef": "medicationCode",
            "mustHave": true
          },
          {
            "attributeRef": "dosage",
            "mustHave": true
          }
        ],
        "filter": [
          [
            {
              "termCodes": [
                {
                  "code": "B01",
                  "system": "http://fhir.de/CodeSystem/bfarm/atc",
                  "version": "2022",
                  "display": "Antithrombotic Agents"
                }
              ],
              "context": {
                "code": "Medication",
                "system": "fdpg.mii.cds",
                "version": "1.0.0",
                "display": "Medication administered"
              }
            }
          ]
        ]
      }
    ]
  }
}