Procedure → OMOP Mapping

FHIR Procedure represents surgical, diagnostic, and therapeutic procedures performed on a patient. It maps primarily to procedure_occurrence, though domain routing may redirect some coded procedures to drug_exposure, device_exposure, measurement, or observation based on the concept's domain_id in the OMOP vocabulary.

Target OMOP Tables

Mapping Strategy

1. Domain routing. Some SNOMED/CPT/OPS procedure codes have domain_id != Procedure in the OMOP vocabulary (e.g., Drug, Observation, Measurement). A full implementation looks up the standard concept's domain and routes accordingly. ETL-German is the most comprehensive, routing to procedure_occurrence, observation, measurement, and drug_exposure. NACHC additionally routes to condition_occurrence. The HL7 IG and omoponfhir do not implement domain routing.

2. Date handling. performed[x] is polymorphic: performedDateTime or performedPeriod. For performedDateTime, the date part goes to procedure_date/procedure_datetime; end date is either the same date (NACHC) or null (ETL-German). For performedPeriod, start maps to procedure_date/procedure_datetime and end maps to procedure_end_date/procedure_end_datetime. OMOP requires at least procedure_date -- skip the resource if no date is available.

3. Status filtering. Recommended: only completed procedures should produce rows. ETL-German is more permissive, accepting in-progress, on-hold, completed, and unknown. Statuses not-done, entered-in-error, stopped, and preparation should always be skipped. omoponfhir does not filter by status at all.

4. Body site. Procedure.bodySite → modifier_concept_id. Requires SNOMED body site → OMOP concept lookup. Take first bodySite[0] entry; remaining entries are lost. ETL-German additionally handles German OPS site localization extensions. Most implementations (omoponfhir, FhirToCdm, HL7 IG) do not map body site at all.

5. Provider. Procedure.performer[].actor -- iterate performers and take the first Practitioner-typed reference for provider_id. Ignore non-Practitioner performers (Organization, Device, etc.). NACHC defaults provider_id to 1 when absent.

6. Vocabulary mapping. Procedure codes come from multiple vocabularies: SNOMED CT (preferred, direct standard concepts), CPT-4 (US billing, standard in OMOP), ICD-10-PCS (US inpatient, non-standard -- requires Maps-to relationship), OPS (German, requires custom lookup), and HCPCS. When multiple code.coding entries exist, implementations differ: ETL-German selects by vocabulary priority (OPS > DICOM > SNOMED), FhirToCdm creates one row per coding, HL7 IG takes the first coding.

7. Device exposure from usedCode. ETL-German is the only implementation that creates device_exposure rows from Procedure.usedCode codings. Other implementations ignore this field entirely.

Reference Implementations

• fhir-omop-ig (HL7) -- Normative IG; FML at refs/refs/fhir-omop-ig/input/maps/Procedure.fml (29 lines). Maps code and performed[x] only. procedure_occurrence_id and person_id are commented-out TODOs. No status filtering, no body site, no provider, no domain routing. Status: draft.
• omoponfhir (Georgia Tech, Java) -- Bidirectional; refs/refs/omoponfhir-omopv5-r4-mapping/src/main/java/edu/gatech/chai/omoponfhir/omopv5/r4/mapping/OmopProcedure.java (515 lines). constructOmop() handles code concept lookup, person, encounter, performer (with specialty update), and performed date. Uses type concept 44786630 (Primary Procedure). No status filtering, no body site, no domain routing. Status: stale (2022).
• FhirToCdm (OHDSI, C#) -- refs/refs/FhirToCdm/FhirToCdmMappings.cs CreateProcedureOccurrence() (lines 407-451). Creates one row per code.coding. Uses type concept 32817 (EHR). Checks domain for Measurement routing. Always casts performed to Period (fails for performedDateTime). Status: low activity.
• ETL-German-FHIR-Core (OHDSI, Java) -- refs/refs/ETL-German-FHIR-Core/src/main/java/org/miracum/etl/fhirtoomop/mapper/ProcedureMapper.java (1140 lines). Most complete implementation: OPS/SNOMED/DICOM vocabulary support, full domain routing (Procedure/Observation/Measurement/Drug), body site + OPS localization extension, device exposure from usedCode, status filtering, incremental updates with delete-and-reinsert. German MII profile-specific. Status: maintained.
• NACHC-fhir-to-omop (Java, DSTU3) -- refs/refs/NACHC-fhir-to-omop/src/main/java/org/nachc/tools/fhirtoomop/omop/person/factory/builder/procedure/OmopProcedureBuilder.java (136 lines). Domain routing to Procedure/Measurement/Observation/Condition. Uses DB-backed concept mapper. Defaults: provider_id=1, quantity=1, modifier_concept_id=0. DSTU3 (not R4). Status: active.
• fhir-x-omop (Python) -- refs/refs/fhir-x-omop/fhir_x_omop/to_omop/procedure_occurrence.py (34 lines). Minimal mapper with all concept_ids hardcoded to 0. Handles performedDateTime only (no Period). Status: early WIP.
• HealthcareLakeETL (PySpark) -- refs/refs/HealthcareLakeETL/mappings/procedure_occurrence.py (44 lines). PySpark column-level transformation. Period.start only. No concept mapping. Status: abandoned.

Status in This Project

Not yet implemented. No src/mapper/procedure.ts exists.