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Import an external OMOP CDM database

This scenario demonstrates how to connect directly to an external PostgreSQL OMOP CDM database, test the connection, preview importable OMOP tables, remap patient identifiers, and import demographics and clinical data into the Patient Journey Gold OMOP database.

Best for: customers who already maintain an OMOP CDM database and want to bring that structured data directly into Patient Journey without file upload.

Step 1: Register the external OMOP source​

  1. In the left navigation, go to Data Integration > Source Registry or the configured ingestion source setup page.
  2. Create a new database source.
  3. Select PostgreSQL Connection as the source type.
  4. Enter the connection details for the external OMOP CDM database.
  5. Confirm that the source database contains the required OMOP CDM schemas and tables.

Step 2: Test the connection and preview OMOP tables​

  1. Run the connection test before starting ingestion.
  2. Confirm that the database is reachable from the Patient Journey Intelligence deployment.
  3. Preview which OMOP tables will be imported.
  4. Review patient, demographic, condition, drug, procedure, observation, visit, and era-related tables where available.
  5. Resolve connection, permission, schema, or table-visibility issues before continuing.

Step 3: Configure patient ID remapping​

  1. Review how patient identifiers from the external OMOP database map to existing Patient Journey records.
  2. Enable auto-remap when imported patient IDs should be reconciled with local target identifiers.
  3. Confirm that ID remapping will not overwrite or duplicate existing patient records.
  4. Review any unmatched, duplicate, or ambiguous patient mappings before import.

Step 4: Import OMOP demographics and clinical data​

  1. Select the OMOP domains that should be imported.
  2. Import demographics and clinical data into the Patient Journey Gold OMOP database.
  3. Monitor import progress, validation messages, skipped records, and failed rows.
  4. Confirm that imported records are merged safely with existing patient data.

Step 5: Generate condition and drug eras where needed​

  1. Decide whether condition and drug eras should be generated during processing.
  2. Enable era generation if optimized longitudinal condition or medication timelines are needed.
  3. Review generated condition and drug eras after processing completes.
  4. Validate that eras align with imported source records and expected OMOP logic.

Step 6: Validate the imported Patient Journey​

  1. Open imported patients in Patient Journey.
  2. Review demographics, visits, conditions, medications, observations, procedures, and eras.
  3. Use Database Explorer to confirm that imported OMOP records are queryable.
  4. Build a small cohort from imported facts to validate downstream usability.
  5. Confirm that imported data is available for Patient Journey, Cohort Builder, Database Explorer, and other OMOP-backed workflows.

Edge cases / limitations​

  • The external database must be reachable from the deployment environment.
  • Database permissions must allow reading the required OMOP schemas and tables.
  • Patient ID remapping should be reviewed carefully to avoid duplicate or incorrectly merged records.
  • OMOP version, vocabulary alignment, and local extensions may affect import completeness.
  • Era generation should be validated when source era tables are missing or regenerated during processing.

Structured FHIR to OMOP for ingesting FHIR bundles directly into OMOP CDM.