AllergyIntolerance → OMOP Mapping

FHIR AllergyIntolerance records patient allergies and intolerances. OMOP has no dedicated allergy table — allergies are stored as observations with allergy-specific SNOMED concepts.

Target OMOP Tables

Mapping Strategy

1. Target table. All implementations agree: AllergyIntolerance → OMOP observation. The allergy substance code maps to observation_concept_id (SNOMED allergy concepts) or value_as_concept_id (substance concept, with a category concept in observation_concept_id). Reaction manifestations can map to value_as_string or create separate observation rows.

2. observation_concept_id strategy. Two approaches exist. omoponfhir uses category-based concept selection: food allergy → 4188027 ("Allergy to food"), medication → 439224 ("Allergy to drug"), default → 40772948 ("Allergy"). This approach places the substance in value_as_concept_id. Other implementations (FhirToCdm, HL7 IG FML) look up the substance code directly in the OMOP vocabulary and place it in observation_concept_id. This project currently uses 0 as a placeholder — vocabulary lookup is required.

3. Date handling. AllergyIntolerance.onsetDateTime → observation_date. Fallback chain: onsetPeriod.start → recordedDate. If none exist, the allergy is skipped (this project) or the encounter date is used (FhirToCdm).

4. Status filtering. clinicalStatus = active should be mapped. inactive and resolved represent historical state and are skipped. verificationStatus = entered-in-error or refuted should always be skipped. When clinicalStatus is absent, map permissively.

5. Allergy type. AllergyIntolerance.type (allergy vs intolerance) and category (food, medication, environment, biologic) inform the observation_concept_id selection in omoponfhir. This project stores type in qualifier_source_value. No standard OMOP concept exists for type/criticality.

6. Reactions. AllergyIntolerance.reaction[].manifestation maps to value_as_string (concatenated display names). The first manifestation could also map to value_as_concept_id with vocabulary lookup. The HL7 IG FML maps reaction manifestation code directly to value_as_concept_id.

7. Provider resolution. recorder (who documented it) and asserter (who states it's true) are both candidates for provider_id. This project prefers asserter, falling back to recorder. omoponfhir uses recorder only.

Reference Implementations

• fhir-omop-ig (HL7) — FML at refs/refs/fhir-omop-ig/input/maps/Allergy.fml (51 lines). Maps code → observation_concept_id, onset → observation_date, reaction.manifestation → value_as_concept_id. Patient/encounter/provider references are commented out (TODO). Status: draft.
• omoponfhir (Georgia Tech, Java) — refs/refs/omoponfhir-omopv5-r4-mapping/src/main/java/edu/gatech/chai/omoponfhir/omopv5/r4/mapping/OmopAllergyIntolerance.java (449 lines). Bidirectional. Category-driven concept selection (food→4188027, medication→439224, default→40772948). Substance → value_as_concept_id. Type concept = 38000280 ("Observation recorded from EHR"). Status: maintained.
• omoponfhir-v54 (Georgia Tech, Java, v5.4) — refs/refs/omoponfhir-v54-r4/omoponfhir-omopv5-r4-mapping/src/main/java/edu/gatech/chai/omoponfhir/omopv5/r4/mapping/OmopAllergyIntolerance.java (450 lines). Identical logic to omoponfhir. Status: maintained.
• FhirToCdm (OHDSI, C#) — refs/refs/FhirToCdm/FhirToCdmMappings.cs lines 453-480 CreateObservation(). Maps AllergyIntolerance → observation via vocabulary lookup on code. Uses recordedDate for date. No status filtering. Minimal field coverage.
• fhir-to-omop-demo (jq) — refs/refs/fhir-to-omop-demo/demo/translate/map/AllergyIntolerance.jq (48 lines). Maps to condition_occurrence (not observation) — divergent approach. Uses recordedDate for start date. Type concept = 32817.
• ETL-German-FHIR-Core — No dedicated AllergyIntolerance mapper.
• NACHC-fhir-to-omop — No dedicated AllergyIntolerance mapper (handles via generic observation).

Status in This Project

Implemented: src/mapper/allergy-intolerance.ts (103 lines). Tests: tests/allergy-intolerance.test.ts (312 lines). Maps substance code, onset date with fallback chain, recorder/asserter, reaction manifestations, type, criticality. Status filtering implemented. Vocabulary lookup is placeholder (concept_id = 0).