omoponfhir / omopv5_4_setup

OMOP v5.4 setup for OMOPonFHIR

How to install PostgreSQL database for OMOPv5.4 using Docker

1. Goto Athena.ohdsi.org to download Vocabularies. ./cpt.sh <your_username>

2. Get DDLs from https://github.com/OHDSI/CommonDataModel

3. Get docker image of PostgreSQL: docker pull postgres

4. Run docker run --name omopv54 -d -p 5432:5432 -e POSTGRES_PASSWORD= --restart unless-stopped postgres:latest

5. Create database and schema create database with owner postgres;

6. Run DDL from ODHSI. DDLs are in CommonDataModel folder. Goto postgresql folder. psql -h localhost -p -U postgres -W -d -f CommonDataModel/OMOP\ CDM\ postgresql\ ddl.txt 5.1 You may want to run the follow if you want to index them. psql -h localhost -p -U postgres -W -d -f CommonDataModel-5.4.0/inst/ddl/5.4/postgresql/<ddl_files>

7. Run DDLs for f_observation_view, f_immunizqtion_view, and f_person omoponfhir_f_person_ddl.txt observation_column_size_change_ddl.txt omoponfhir_v5.4_f_observation_view_ddl.txt omoponfhir_v5.2_f_immunization_view_ddl.txt

8. Load vocabularies downloaded from Athena. change the ddl in VocaImport/ to point to the vocabulary files. And change COPY to \copy

9. Use fhir_names ETL to load f_person if your database already has data in it. Read the instruction in fhir_names/ folder.

10. Indexing all IDs in OMOP tables