A demo to translate synthea FHIR data to OMOP!
This demo was prepared in advance of the 2024 FHIR DevDays in Minneapolis.
Many researchers and developers will have access to either FHIR or OMOP, but not necessarily both. And for those with access to both, these two systems may not be sourced with the same data.
At Mayo Clinic we have made great use of OMOPCDM data for AI applications, but our conversion solution is not easy to share since it relies on cloud services for the source data, conversion process, and destination.
This demo was written to serve the FHIR and OMOP communities by providing an easy way to create a FHIR server loaded with non-trivial data, demonstrate one approach for conversion of FHIR resources into OMOPCDM records, and to encourage further exploration of this conversion process.
To get started, clone this repo and the barabo/fhir-jq repo.
mkdir ~/demo && cd $_
gh repo clone barabo/fhir-to-omop-demo
gh repo clone barabo/fhir-jq
Each of the directories in this repo contain instructions and notes, but you should understand the basic flow of instructions before you begin.
You will:
- Download the MITRE Coherent data set and extract it into
data/coherent - Download terminology data from Athena and place it into
data/athena - Load the terminology into an empty OMOPCDM database by running the script provided in
demo/omopcdm - Load the Coherent FHIR resources into a local hapi server by running the scripts in
demo/hapi - Bulk Export the data from hapi, placing the ndjson files into
data/bulk-export/ - Install
jqand configure it to use the module provided infhir-jq/module - Translate FHIR-to-OMOP by running the script in
demo/translate - Load the OMOPCDM data by running the script in
demo/load
Begin with the README.md in the fhir-to-omop-demo/demo directory!
This demo uses the MITRE Health Coherent data set, and should be cited according to their wishes. Thank you, MITRE Health!
If you download and use this data, be sure to remember to cite them, too!
Walonoski J, Hall D, Bates KM, Farris MH, Dagher J, Downs ME, Sivek RT, Wellner B, Gregorowicz A, Hadley M,
Campion FX, Levine L, Wacome K, Emmer G, Kemmer A, Malik M, Hughes J, Granger E, Russell S.
The “Coherent Data Set”: Combining Patient Data and Imaging in a Comprehensive, Synthetic Health Record.
Electronics. 2022; 11(8):1199.