Medication

— maps to 1 OMOP table

OMOP Table	Status	Mapped
drug_exposure primary The FHIR Medication resource is a vocabulary/codeable-concept resource, not a medication event. It does NOT directly produce a drug_exposure row. Instead, its code and ingredient data are resolved into drug_concept_id and drug_source_value on drug_exposure rows produced by the four event resources (MedicationRequest, MedicationDispense, MedicationAdministration, MedicationStatement). This edge documents how Medication fields contribute to drug_exposure columns when referenced.	documented	3 fields	detail →

Medication (Vocabulary Resource) → OMOP Mapping

The FHIR Medication resource is a vocabulary / codeable concept, not a medication event. It does NOT directly produce a drug_exposure row. Instead, it gets resolved into the drug_concept_id and drug_source_value of drug_exposure rows produced by the four event resources.

The four event resources that DO produce drug_exposure rows are:

MedicationRequest — prescription/order stage.
MedicationDispense — pharmacy dispensing stage.
MedicationAdministration — inpatient administration stage.
MedicationStatement — patient self-report stage.

What `Medication` Carries

A FHIR Medication resource may include:

code — CodeableConcept with RxNorm / ATC / NDC / SNOMED codings (the primary contribution to drug_concept_id).
form — dosage form (tablet, capsule, etc.).
ingredient[] — active substance(s) and strength.
manufacturer, batch, etc.

Only code and (for some implementations) ingredient are used in OMOP mapping. The rest is dropped.

Resolution Strategies

When an event resource (MedicationRequest/Dispense/Administration/Statement) carries medicationReference rather than inline medicationCodeableConcept, the implementation must resolve the reference to extract the code:

Strategy	Implementations	Notes
Contained reference (`#id`)	omoponfhir	Iterates the event resource's `contained[]` array to find the Medication by ID fragment. Extracts `Medication.code` and falls back to `Reference.display` if no code is found.
Bundle merge / two-phase	fhir-to-omop-demo	The event mapper produces a partial `drug_exposure` row; a separate `Medication.jq` produces matching partial rows; rows are merged by ID in a post-processing phase.
Pre-indexed map	ETL-German	`MedicationMapper` walks all Medication resources up front and builds a `medication_id_map` keyed by resource ID. Event resource mappers look up references in this map. ATC codes are extracted from the Medication's ingredients.
Inline-only (skip references)	FhirToCdm, NACHC, fhir-x-omop, this project	Process `medicationCodeableConcept` only. Skip / return null when the event resource has only `medicationReference`.

Vocabulary Mappings

The Medication resource's code field carries codes from the same vocabularies used in inline medicationCodeableConcept:

RxNorm (US, primary OMOP vocabulary).
NDC (US, National Drug Code).
ATC (Europe, used by ETL-German for German MII data).
SNOMED CT (product codes).

Vocabulary priority order for selecting the best coding: RxNorm > NDC > ATC > SNOMED > first available.

OMOP Output Path

The Medication resource itself does NOT produce a row in any OMOP table. Its content flows into the event resources' drug_exposure rows:

FHIR `Medication.*`	OMOP field on `drug_exposure` (set by event mapper)
`Medication.code.coding[best].code`	`drug_source_value`
`Medication.code.coding[best]` (after vocab lookup)	`drug_concept_id`, `drug_source_concept_id`
`Medication.ingredient[].itemCodeableConcept` (ATC)	Used by ETL-German as the source for `drug_source_value`
`Medication.form`	Not directly mapped to OMOP. Dose form is captured implicitly via `drug_concept_id` (RxNorm products encode form).

Reference Implementations (Medication-resolution aspects only)

omoponfhir-omopv5-r4-mapping (Georgia Tech, Java) — Resolves contained #-references in event resources. Code paths: OmopMedicationRequest.java lines 547-597 (medication resolution including contained ref), OmopMedicationStatement.java lines 751-805 (same logic).
fhir-to-omop-demo (jq) — Two-phase merge. refs/refs/fhir-to-omop-demo/demo/translate/map/Medication.jq (71 lines) produces partial drug_exposure rows with concept info only; these are merged by ID with rows from MedicationRequest.jq.
ETL-German-FHIR-Core (OHDSI, Java) — Pre-indexed map. refs/refs/ETL-German-FHIR-Core/src/main/java/org/miracum/etl/fhirtoomop/mapper/MedicationMapper.java (274 lines). Walks all Medication resources, builds medication_id_map for reference resolution, extracts ATC codes from ingredients.
FhirToCdm (OHDSI, C#), NACHC, fhir-x-omop, this project — Inline-only; medicationReference is skipped.
HL7 IG FML (refs/refs/fhir-omop-ig/input/maps/medication.fml) — Maps MedicationStatement only and assumes inline coding. Does not address Medication resource resolution.

Status in This Project

medicationReference resolution is not implemented. Both MedicationRequest and MedicationStatement mappers return null when only medicationReference is present.
The Medication resource itself is not pre-indexed or otherwise consumed.
TODO: implement contained-reference resolution (omoponfhir-style) as a minimum, and consider pre-indexing for Bundle-level inputs.