OMOP to FHIR Bulk Data API used for MENDS
summary
ESP-based surveillance is provisioning ESP data marts from OMOP by running an OMOP to FHIR NDJSON transform via Google Cloud Dataflow and a Whistle transform, then loading huge NDJSON files (observation NDJSON ~1 TB for 2017–present) into Postgres JSONB and parsing with a Python/Django app. A FHIR Bulk Data client for ESP handles monthly batch exports of patient encounter condition observation claim medicationrequest and immunization resources. Work is functional for one regional partner; parsing code is in-progress and Health Data Compass will publish its OMOP->Bulk service.
AI-written summary · about
chapters (18)
- 0:00Introduction
- 0:59Presentation Overview
- 1:45What is MENDS
- 2:28What is OMOP Health
- 3:30How does it work
- 5:05MENDS partners
- 5:32Data mart provisioning
- 7:01Health Data Compass
- 7:50Data Flow
- 8:49Fire Bulk Data Client
- 9:37Code
- 10:24Conclusions
- 11:10Barriers
- 12:23Contact Information
- 13:58Fire Transform
- 14:34Data Model
- 16:41Questions
- 17:50Trigger process
related talks
30mCMS: Data at the Point of Care
47mMapping FHIR to OMOP Using Open Source Tools
35mBulk Data
46mFHIR Bulk Data API + What's New in v2.0
42mFHIR Bulk Data API
46mThe FHIR Bulk Data API and what's new in v2!
44mOpenMDM - Data Management for SDV
32mMake EHR Data Available for Research and Public Health (MedMorph)