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Structured FHIR to OMOP

This scenario demonstrates how to ingest structured FHIR R4 clinical data directly into OMOP CDM records, without requiring NLP processing when the source bundle already contains the clinical facts needed for downstream workflows.

Best for: fast structured-data ingestion, FHIR-native deployments, and demos where the source bundle already contains coded clinical facts.

Step 1: Prepare the FHIR source​

  1. Confirm that the source contains valid FHIR R4 resources.
  2. Review the available resource types, such as Conditions, Medications, Observations, Procedures, Encounters, and Visits.
  3. Confirm whether Patient resources should be imported for demographics.
  4. Validate that patient identifiers and encounter references can be linked consistently.

Step 2: Run structured FHIR ingestion​

  1. Register or select the FHIR source in the ingestion workflow.
  2. Configure the ingestion job for structured FHIR processing.
  3. Select the clinical resource types that should be mapped into OMOP.
  4. Start the ingestion job.
  5. Monitor ingestion progress, validation messages, and failed-resource counts.

Step 3: Map FHIR resources to OMOP CDM​

  1. Convert FHIR clinical resources into the appropriate OMOP domains.
  2. Map conditions into condition_occurrence.
  3. Map medications into drug-related OMOP records.
  4. Map observations, labs, procedures, encounters, and visits into their corresponding OMOP tables.
  5. Preserve source references so records can be traced back to the original FHIR bundle.

Step 4: Merge structured records into the production OMOP database​

  1. Review mapped records before publishing where validation is available.
  2. Resolve duplicate or conflicting records if the same clinical facts already exist.
  3. Merge validated records into the production OMOP database.
  4. Confirm that the imported data is available to Patient Journey, Cohort Builder, Database Explorer, and other downstream modules.

Step 5: Validate the Patient Journey output​

  1. Open a patient represented in the FHIR bundle.
  2. Review demographics, conditions, medications, observations, procedures, encounters, and visits.
  3. Confirm that structured clinical events appear in the expected timeline and OMOP-backed views.
  4. Use Database Explorer or cohort filters to validate that the imported facts are queryable.

Edge cases / limitations​

  • This path is best when the FHIR bundle already contains the clinical facts needed for analysis.
  • Free-text notes still require document ingestion and NLP processing if facts must be extracted from narrative text.
  • Mapping quality depends on source coding, resource completeness, patient references, and terminology normalization.
  • Patient demographic import should be configured deliberately when Patient resources are included.

Import an external OMOP CDM database for customers who already run OMOP CDM directly.