MedicationRequest → OMOP Mapping

MedicationRequest represents the prescription/order stage of the medication lifecycle. It is the richest of the four FHIR medication-event resources for OMOP purposes because it carries dispense, refill, and supply-duration metadata that the other three lack.

Source FHIR Resource

Target OMOP Tables

Mapping Strategy

1. Status / intent filtering. entered-in-error should always be skipped. This project also skips stopped, on-hold, draft, and unknown. Non-order intents (proposal, plan) are filtered out -- only order, original-order, reflex-order, filler-order, instance-order produce rows. omoponfhir maps all statuses and intents except entered-in-error.

2. Medication resolution. medication[x] can be a CodeableConcept (inline code) or a Reference to a Medication resource. omoponfhir resolves contained #-references; fhir-to-omop-demo merges by ID in a post-processing phase; this project and most others handle inline codes only. RxNorm is the standard OMOP drug vocabulary (US); ATC is used in European data.

3. Vocabulary lookup. The drug_concept_id requires mapping FHIR medication codes (RxNorm, ATC, NDC, SNOMED) to OMOP standard concepts via the OMOP vocabulary tables. Route codes (SNOMED to OMOP Route domain) also require lookup. Only omoponfhir performs runtime concept lookups for MedicationRequest; FhirToCdm uses pre-built vocabulary files; this project uses placeholder 0.

4. Date handling. authoredOn maps to drug_exposure_start_date. dispenseRequest.validityPeriod.end maps to drug_exposure_end_date (fallback to start date when absent). FhirToCdm derives dates from the linked VisitOccurrence. NACHC falls back to encounter start date when authoredOn is null.

5. Dosage parsing. OMOP captures only: quantity (dose per administration), days_supply, sig (free-text instructions), route_concept_id. Most implementations extract dose quantity and route from the first dosageInstruction[], ignoring timing complexity.

6. Days supply. Calculated from MedicationRequest.dispenseRequest.expectedSupplyDuration. This project converts UCUM duration units (h, d, wk, mo, a). No reference implementation populates this field.

7. Refills. MedicationRequest.dispenseRequest.numberOfRepeatsAllowed maps to refills. omoponfhir reads this from the dispenseRequest block. Only applicable to MedicationRequest.

8. Type concept. Constant 38000177 ("Prescription written"). fhir-to-omop-demo uses 32838 (EHR prescription); FhirToCdm and ETL-German use 32817 (EHR / CLAIM).

Reference Implementations

• omoponfhir-omopv5-r4-mapping (Georgia Tech, Java) -- OmopMedicationRequest.java (746 lines). Most complete: RxNorm concept lookup, contained reference resolution, route concept lookup, dosage parsing, dispense-request fallback for refills/quantity, provider from recorder. Status: stale (2022).
• FhirToCdm (OHDSI, C#) -- FhirToCdmMappings.cs CreateDrugExposure() (lines 310-405, MedicationRequest branch lines 322-373). Vocabulary file lookup. Dates derived from VisitOccurrence. Sig from dosageInstruction[0].text. Status: low activity.
• fhir-to-omop-demo (jq) -- MedicationRequest.jq (81 lines). Two-phase merge approach: partial rows from MedicationRequest are joined with partial rows from Medication.jq by ID. Pre-computed vocabulary concepts. Type concept 32838 (EHR prescription). Status: maintained.
• NACHC-fhir-to-omop (Java, DSTU3) -- MedicationRequestParser.java (155 lines). Parses medication code, status, intent, dates. Falls back to encounter start date when authoredOn is null. Status: active.

Status in This Project

• src/mapper/medication.ts -- MedicationRequest mapper (93 lines). Implements: status/intent filtering, inline medication only, days_supply from expectedSupplyDuration, refills, sig, route source value.
• drug_concept_id is hardcoded to 0 (no vocabulary lookup).
• route_concept_id is hardcoded to null (source value only).
• medicationReference resolution is not implemented (returns null).

Related Resources

• MedicationDispense -- pharmacy dispensing stage.
• MedicationAdministration -- inpatient administration stage.
• MedicationStatement -- patient self-report stage.
• Medication -- vocabulary/codeable concept resource (not an event).