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enchilada

enchilada is a local FHIR R4 terminology server that translates FHIR codes to OMOP concept IDs. It is designed to run alongside matchbox as the txServer for FHIR Mapping Language (FML) translate() calls during FHIR-to-OMOP ETL.

Architecture

FHIR Patient/Observation/...
        │
        ▼
   matchbox ($transform)
        │  FML translate()
        ▼
   enchilada (/r4/ConceptMap/$translate)
        │
        ▼
   OMOP concept_id

enchilada is backed by:

  • CONCEPT.csv from an Athena vocabulary download (SNOMED, LOINC, RxNorm, ICD-10-CM, …)
  • Supplemental TSV files for FHIR administrative code systems (AdministrativeGender, AllergyIntoleranceCategory, v3-ActCode, CVX, …)

Quick start

pip install -e .
# edit config.yaml to point at your CONCEPT.csv and SQLite path
python -m enchilada

See Configuration for the full config file reference.

Supported FHIR version

enchilada supports R4 only. R5 requests are not handled.