Mapping FHIR to OMOP Using Open Source Tools

on YouTube ↗47m

" summary

Demonstrates an open source pipeline that takes FHIR STU3 transaction bundles from a HAPI test server, runs a configurable FHIR-to-OMOP converter (deployed locally or on Google Cloud), and writes OMOP CDM v6 tables into BigQuery using OHDSI vocabularies and the concept_map feedback loop. Shows actual pain points: medication administration vs dispense/request, observation vs measurement domain choice, missing person demographics. Converter produces usable CDM output but requires iterative reconfiguration of mappings and vocabulary lookups.

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" chapters (7)

1. 0:00Session introduction
2. 1:09Project overview
3. 6:33History and goals of OMOP
4. 12:05OMOP data model structure
5. 25:37Incremental ETL pipeline
6. 31:13FHIR and OMOP mapping challenges
7. 37:01FHIR conversion and Q&A

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