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RxNormToFHIR

The script performs the following functions:

  1. Look up each RxNorm concept against its relationships and attributes
  2. Translate each concept into a pair of FHIR Medication and MedicationKnowledge resources
  3. Load resources as bundles into a target FHIR server (tested with HAPI-FHIR JPA Server 3.7.0) or into JSON files for local testing.

RxNorm relationships processed include (ref):

  • has_ingredient
  • has_dose_form
  • consists_of
  • contains
  • isa
  • has_form

RxNorm attributes processed include (ref):

  • RXN_BOSS_STRENGTH_NUM_VALUE
  • RXN_BOSS_STRENGTH_NUM_UNIT
  • RXN_BOSS_STRENGTH_DENOM_VALUE
  • RXN_BOSS_STRENGTH_DENOM_UNIT
  • RXN_STRENGTH

The goal is to create a FHIR server to be used as a dictionary backend for natural language processing (NLP).

Script output:

Reading RxNorm concepts file	4.522 s
Reading RxNorm relationships file	13.07 s
Reading RxNorm attributes file	14.38 s
Writing FHIR Substance resources	312.3 ms
Writing FHIR Medication resources	5.154 s
Writing FHIR SearchParameter resources	88.20 ms
[main] INFO ca.uhn.fhir.util.VersionUtil - HAPI FHIR version 3.7.0 - Rev f2560071c8
[main] INFO ca.uhn.fhir.context.FhirContext - Creating new FHIR context for FHIR version [R4]
Writing Substance bundle (size: 6913) to local file	4.416 s
Writing Medication bundle (size: 90723) to local file	6.040 s
Writing MedicationKnowledge bundle (size: 90723) to local file	6.793 s
Units of measure detected: [%, ACTUAT, AU, BAU, CELLS, HR, MCI, MEQ, MG, ML, MMOL, PNU, SQCM, UNT]
Total time taken 6.801 s

TODO

  • Load RxNorm ingredients as FHIR Substance resources
  • Load RxNorm ingredient synonyms as extensions in FHIR Substance resources
  • Load RxNorm drug brand names as extensions in FHIR Medication resources
  • Load RxNorm drug parent concepts in FHIR MedicationKnowledge resources
  • Load RxNorm drug synonyms in FHIR MedicationKnowledge resources

See also: MedServe