Skip to content

Latest commit

 

History

History
37 lines (27 loc) · 2.19 KB

README.md

File metadata and controls

37 lines (27 loc) · 2.19 KB
Raw

OMOP-on-FHIR DEMO

If you are a student working with the Georgia Tech CS6440 course, for help with this demo please reach out to Elizabeth.Shivers@gtri.gatech.edu. If you are with another university or would like general OMOP on FHIR information, please email info@omoponfhir.com.

! Warning: The /resources folder contains in progress work to streamline loading Synthea transaction bundles. It is not currently functional and should be disregarded. !

Quick Start

Step 1 - Download Athena Vocab

Go to https://athena.ohdsi.org/search-terms/start. Go to Download.

Select the following Vocabularies to Download:

  • LOINC
  • SNOMED
  • RxNorm
  • Gender (OMOP Gender)
  • Race (Race and Ethnicity Code Set (USBC))

Step 2 - Add Vocab to Build Path

Extract the .CSV files from the zip provided by Athena. Place the CSVs in the /vocab directory (which should be available when you clone with a place holder file inside it).

Step 3 - Run Docker

With Docker Desktop/Engine running, execute the following command: docker compose up

Troubleshooting

If you run into an error, cancel your running container with CTRL+C in the terminal. Then be sure to remove the partially configured container with docker compose down before running the up command again.

Health Check Script

The OMOP CDM database image used includes a health check script which allows the OMOP on FHIR container to wait until the f_person tables are available prior to starting. This shows up as an expected "error" in the logs, as follows:

2023-06-30 16:58:46.481 UTC [91] ERROR:  relation "f_person" does not exist at character 15
2023-06-30 16:58:46.481 UTC [91] STATEMENT:  SELECT * FROM f_person;

This message can be disregarded.

Please note this script may not work consistently in all environments, and has been observed to not always function as expected in Non-WSL Windows deployments, starting the OMOP on FHIR container prior to the required dependencies being setup. In such a case, you may have to stop the containers after the database has been loaded fully and rerun them per the troubleshooting section of this file. (It should pick up with the database fully loaded and should not impact the operation of the containers.)