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