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Add FHIR resolver example script#11

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alex-omophub merged 1 commit intomainfrom
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Apr 10, 2026
Merged

Add FHIR resolver example script#11
alex-omophub merged 1 commit intomainfrom
develop

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@alex-omophub alex-omophub commented Apr 10, 2026

  • Introduced a new script fhir_resolver.py that demonstrates FHIR-to-OMOP concept resolution using the OMOPHub SDK.
  • The script includes examples for resolving SNOMED, ICD-10-CM, LOINC, RxNorm codes, and text-only semantic searches.
  • Added functionality for direct standard lookups, non-standard code mapping, and Phoebe recommendations.
  • Supports batch resolution and asynchronous usage for improved performance.

Summary by cubic

Adds an example script to demonstrate FHIR-to-OMOP concept resolution with omophub, covering direct lookups, mappings, semantic search, batch, and async usage. Helps users map FHIR system+code or text to OMOP concepts, target tables, and optional Phoebe recommendations in one call.

  • New Features
    • Direct SNOMED/LOINC/RxNorm lookups; ICD-10-CM “Maps to” traversal; vocabulary_id bypass.
    • Text-only semantic search; mapping quality signal; Phoebe recommendations.
    • Batch resolution with per-item errors; async client examples.
    • CodeableConcept resolution with vocabulary preference and text fallback.

Written for commit 9292470. Summary will update on new commits.

- Introduced a new script `fhir_resolver.py` that demonstrates FHIR-to-OMOP concept resolution using the OMOPHub SDK.
- The script includes examples for resolving SNOMED, ICD-10-CM, LOINC, RxNorm codes, and text-only semantic searches.
- Added functionality for direct standard lookups, non-standard code mapping, and Phoebe recommendations.
- Supports batch resolution and asynchronous usage for improved performance.
@alex-omophub alex-omophub merged commit 72bb565 into main Apr 10, 2026
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codecov bot commented Apr 10, 2026

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✅ All modified and coverable lines are covered by tests.

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