FHIR to OMOP FHIR IG
1.0.0-ballot - INFORMATIVE 1 - Ballot
FHIR to OMOP FHIR IG
1.0.0-ballot - INFORMATIVE 1 - Ballot
This page is part of the Vulcan FHIR to OMOP FHIR Implementation Guide (v1.0.0-ballot: INFORMATIVE 1 Ballot 1) based on FHIR (HL7® FHIR® Standard) v5.0.0. No current official version has been published yet. For a full list of available versions, see the Directory of published versions
| Page standards status: Informative |
A FHIR terminology server operates as a specialized collection of functions built upon FHIR CodeSystem, ValueSet, and ConceptMap resources, specifically designed to support the complex terminology requirements inherent in transforming FHIR resources into OMOP-compliant data. (See: FHIR Terminology Service, Basic Concepts) This greatly reduces the need for implementation teams and ETL developers to be experts in source terminologies and cross-terminology relationships to OMOP concept targets essential for compliant OMOP data normalization. Further, utilization of a terminology server greatly reduces the need for manual mapping labor and provides more consistent and uniform mapping results.
FHIR terminology servers, like Echidna serve as bridge infrastructure that enable automated transformation between FHIR data sources and the OMOP CDM. Core functionality for FHIR to OMOP transformation centers on concept lookup and translation operations. The Echidna server examples below enable systems to resolve FHIR-encoded clinical concepts to their corresponding OMOP standard concepts, retrieve concept relationships necessary for accurate domain assignment, and access the hierarchical mappings required for proper OMOP vocabulary integration.
The FHIR CodeSystem/$lookup provides additional information about a concept. Given a concept ID, e.g. 1567956 we can lookup its properties:
Request:
curl 'https://echidna.fhir.org/r5/CodeSystem/$lookup' \
--request POST \
--header 'Content-Type: application/json' \
--data '{
"resourceType": "Parameters",
"parameter": [
{
"name": "code",
"valueCode": "1576196"
},
{
"name": "system",
"valueUri": "https://fhir-terminology.ohdsi.org"
},
{
"name": "property",
"valueString": "domain-id"
},
{
"name": "property",
"valueString": "standard-concept"
},
{
"name": "property",
"valueString": "Maps to"
}
]
}'
Response:
{
"resourceType": "Parameters",
"parameter": [
{
"name": "system",
"valueUri": "https://fhir-terminology.ohdsi.org"
},
{
"name": "name",
"valueString": "OMOP Concepts"
},
{
"name": "version",
"valueString": "20250227"
},
{
"name": "code",
"valueCode": "1576196"
},
{
"name": "display",
"valueString": "Family history of ischemic heart disease and other diseases of the circulatory system"
},
{
"name": "designation",
"part": [
{
"name": "language",
"valueCode": "en"
},
{
"name": "value",
"valueString": "Family hx of ischem heart dis and oth dis of the circ sys"
}
]
},
{
"name": "property",
"part": [
{
"name": "code",
"valueCode": "domain-id"
},
{
"name": "value",
"valueCode": "Observation"
}
]
},
{
"name": "property",
"part": [
{
"name": "code",
"valueCode": "standard-concept"
},
{
"name": "value",
"valueCode": ""
}
]
},
{
"name": "property",
"part": [
{
"name": "code",
"valueCode": "Maps to"
},
{
"name": "value",
"valueCoding": {
"code": "4148407"
}
}
]
}
]
}
Note: this concept is non-standard (i.e. standard-concept is not "S").
To find standard concept(s) it maps to, refer to the "Maps to" property in the above response.
The value for this property is the concept ID which can be looked up separately:
Request:
curl 'https://echidna.fhir.org/r5/CodeSystem/$lookup' \
--request POST \
--header 'Content-Type: application/json' \
--data '{
"resourceType": "Parameters",
"parameter": [
{
"name": "code",
"valueCode": "4148407"
},
{
"name": "system",
"valueUri": "https://fhir-terminology.ohdsi.org"
}
]
}'
Response:
{
"resourceType": "Parameters",
"parameter": [
{
"name": "system",
"valueUri": "https://fhir-terminology.ohdsi.org"
},
{
"name": "name",
"valueString": "OMOP Concepts"
},
{
"name": "version",
"valueString": "20250227"
},
{
"name": "code",
"valueCode": "4148407"
},
{
"name": "display",
"valueString": "FH: Cardiovascular disease"
},
{
"name": "designation",
"part": [
{
"name": "language",
"valueCode": "en"
},
{
"name": "value",
"valueString": "FH: CVS disorder"
}
]
},
{
"name": "designation",
"part": [
{
"name": "language",
"valueCode": "en"
},
{
"name": "value",
"valueString": "Family history of cardiovascular disease"
}
]
},
{
"name": "designation",
"part": [
{
"name": "language",
"valueCode": "en"
},
{
"name": "value",
"valueString": "Family history: Cardiovascular disease"
}
]
},
{
"name": "designation",
"part": [
{
"name": "language",
"valueCode": "en"
},
{
"name": "value",
"valueString": "Family history: Cardiovascular disease (situation)"
}
]
},
{
"name": "designation",
"part": [
{
"name": "language",
"valueCode": "es"
},
{
"name": "value",
"valueString": "antecedente familiar de cardiovasculopatía"
}
]
},
{
"name": "designation",
"part": [
{
"name": "language",
"valueCode": "es"
},
{
"name": "value",
"valueString": "antecedente familiar de enfermedad cardiovascular"
}
]
},
{
"name": "designation",
"part": [
{
"name": "language",
"valueCode": "es"
},
{
"name": "value",
"valueString": "antecedente familiar de enfermedad cardiovascular (situación)"
}
]
},
{
"name": "property",
"part": [
{
"name": "code",
"valueCode": "concept-id"
},
{
"name": "value",
"valueInteger": 4148407
}
]
},
{
"name": "property",
"part": [
{
"name": "code",
"valueCode": "source-concept-code"
},
{
"name": "value",
"valueCoding": {
"code": "266894000",
"system": "http://snomed.info/sct"
}
}
]
},
{
"name": "property",
"part": [
{
"name": "code",
"valueCode": "domain-id"
},
{
"name": "value",
"valueCode": "Observation"
}
]
},
{
"name": "property",
"part": [
{
"name": "code",
"valueCode": "vocabulary-id"
},
{
"name": "value",
"valueCode": "SNOMED"
}
]
},
{
"name": "property",
"part": [
{
"name": "code",
"valueCode": "concept-class-id"
},
{
"name": "value",
"valueCode": "Context-dependent"
}
]
},
{
"name": "property",
"part": [
{
"name": "code",
"valueCode": "standard-concept"
},
{
"name": "value",
"valueCode": "S"
}
]
},
{
"name": "property",
"part": [
{
"name": "code",
"valueCode": "inactive"
},
{
"name": "value",
"valueBoolean": false
}
]
},
{
"name": "property",
"part": [
{
"name": "code",
"valueCode": "valid-start-date"
},
{
"name": "value",
"valueDate": "2002-01-31"
}
]
},
{
"name": "property",
"part": [
{
"name": "code",
"valueCode": "valid-end-date"
},
{
"name": "value",
"valueDate": "2099-12-31"
}
]
},
{
"name": "property",
"part": [
{
"name": "code",
"valueCode": "invalid-reason"
},
{
"name": "value",
"valueCode": ""
}
]
}
]
}
The FHIR ConceptMap/$translate operation will provide the cross-walk from a source system to OMOP that's stored in a ConceptMap Resource. Given a source code and system, e.g.:
{
"system": "http://hl7.org/fhir/sid/icd-10-cm",
"code": "E11"
}
we can translate to the corresponding OMOP concept ID by using the "translate" operation:
Request:
curl 'https://echidna.fhir.org/r5/ConceptMap/$translate' \
--request POST \
--header 'Content-Type: application/json' \
--data '{
"resourceType": "Parameters",
"parameter": [
{
"name": "sourceCoding",
"valueCoding": {
"system": "http://hl7.org/fhir/sid/icd-10-cm",
"code": "E11"
}
},
{
"name": "targetSystem",
"valueUri": "https://fhir-terminology.ohdsi.org"
}
]
}'
Response:
{
"resourceType": "Parameters",
"parameter": [
{
"name": "result",
"valueBoolean": true
},
{
"name": "match",
"part": [
{
"name": "relationship",
"valueCode": "equivalent"
},
{
"name": "concept",
"valueCoding": {
"code": "1567956",
"system": "https://fhir-terminology.ohdsi.org",
"version": "20250227"
}
}
]
}
]
}
The resulting concept ID is 1567956.
IG © 2023+ HL7 International / Biomedical Research and Regulation. Package hl7.fhir.uv.omop#1.0.0-ballot based on FHIR 5.0.0. Generated 2025-07-29
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