ETL for Swedish Electronic Health Records

Requirements

• PostgreSQL and psql
• Python 3
• OMOP tables configured (see below)

Setup OMOP CDM database like this: CREATE DATABASE ohdsi; CREATE SCHEMA cdm5;

Get this OMOP CDM V5 release: https://github.com/OHDSI/CommonDataModel/tree/d4a4d175fdf90c7d5effeafd5eae0e4b035b6137/PostgreSQL

Download the latest OMOP vocabulary from http://athena.ohdsi.org/.

Then open psql in the commandline and execute the following:

• SET search_path TO cdm5,public;
• \i './CommonDataModel/PostgreSQL/OMOP CDM ddl - PostgreSQL.sql’
• \i './CommonDataModel/PostgreSQL/VocabImport/OMOP CDM vocabulary load - PostgreSQL.sql'

Add source data

• Open the source_tables folder
• Put the patient, drug, death and lisa registers (csv files) in the corresponding subfolders
• Make sure the filenames correspond with files in the overview_source_files.csv file (except for the drug registers)

Execute scripts

• Navigate to the folder
• Open bash and execute sh ./execute_etl.sh <database_name> <user_name> <encoding>

Licence

Published under Apache 2.0 licence.