Map FHIR resources to OMOP CDM v5.4

Maps a FHIR R4 resource or Bundle into OMOP Common Data Model v5.4 rows
(person, visit_occurrence, condition_occurrence, drug_exposure,
procedure_occurrence, measurement, observation).

Resource support is intentionally limited to the OMOP tables returned by
this endpoint:

  • Patient -> person
  • Encounter -> visit_occurrence
  • Condition -> condition_occurrence
  • Procedure -> procedure_occurrence
  • MedicationRequest, MedicationStatement, and
    MedicationAdministration -> drug_exposure
  • Immunization -> drug_exposure
  • Observation with a numeric valueQuantity, valueInteger, or
    numeric-looking valueString (for example "<2") -> measurement
  • non-numeric Observation -> observation
  • AllergyIntolerance -> observation

Medication is supported only as reference data for medication
resources; it is not emitted as its own row because OMOP CDM has no
Medication table. Other reference/admin resources such as Practitioner,
Organization, Location, Coverage, and Claim, and clinical
workflow/document resources such as DiagnosticReport, ServiceRequest,
CarePlan, DocumentReference, Composition, Specimen, and
DeviceUseStatement, are currently accepted in a Bundle but are not
shaped into OMOP rows. Unsupported resource types are ignored rather than
listed under dropped; dropped is reserved for supported resource types
that were missing the subject/patient, code, or medication reference data
needed to produce a valid row.

Each resource's primary clinical coding is resolved to a standard OMOP
concept_id. Alongside the OMOP rows grouped by table (tables), the
response carries mappings (how each source coding resolved, linked back
to the row it produced), dropped (resources that could not be shaped
into a row), vocab_version (the OMOP vocabulary release codes were
resolved against), and a small summary of the resolution outcomes.

A concept_id of 0 is reported, not omitted (OMOP "no matching
concept" semantics): it covers both a coding with no standard match
(UNMAPPED) and an unverified suggestion for a text-only resource
(UNCHECKED). Only the primary clinical coding is resolved, so
gender/race/ethnicity/visit/value/unit concept_ids are
always 0; the one populated non-resolved concept is measurement
operator_concept_id, set from a value comparator (<, <=, >, >=)
rather than the resolver. Each *_source_value carries the verbatim FHIR
coding (system#code), and *_type_concept_id is set to 32817 (EHR).

Medication codes are resolved whether they appear inline
(medicationCodeableConcept) or via a medicationReference to a contained,
relative (Type/id), or bundle-entry (urn:uuid) Medication resource.
Resources that cannot be shaped into a row — a medication with no usable
code, resolvable reference, or display, or any clinical resource whose
subject/patient reference cannot be tied to a person — are reported under
dropped rather than emitted as blank rows. The
bundle must contain at least one Patient resource.

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Body Params
fhir_resources
object
required

FHIR resources (single resource or Bundle). Must contain at least one
Patient resource. Supported row-producing resources are Patient,
Encounter, Condition, Procedure, MedicationRequest,
MedicationStatement, MedicationAdministration, Immunization,
Observation, and AllergyIntolerance. Standalone Medication resources
are consumed by medication references rather than mapped to their own
table. Other resource types are accepted but ignored.

Responses

401

Unauthorized

500

Internal server error

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