OMOP

Getting Started:

To run Carrot-Mapper you need a Postgres database running a schema called "OMOP", based on the OMOP CDM v5.4.0.

What is the OMOP CDM?

For an introduction to the OMOP CDM, see:

• OHDSI Website
• EHDEN Academy OMOP Course

Run locally

The CDM R package can be used to create the DDL scripts and instantiate the tables.

If an OMOP vocabulary has not been supplied to populate the tables, you can download them from Athena.

If you would rather not use the R package, here's a manual approach, each database step can also be replicated using a database tool such as PGAdmin or Datagrip.

1. Download the pregenerated OMOP v5.4.0 DDL's for Postgres.
2. Change the DDLs to use OMOP as a schema, for example using sed: sed -i '' 's/@cdmDatabaseSchema/omop/g' OMOPCDM_postgresql_5.4_ddl.sql
3. Copy the DDLSs, and vocabulary files to the postgres container: docker cp <PATH> carrot-mapper-dev-db-1
4. Access the database container's shell: docker exec -it carrot-mapper-dev-db-1 bash
5. Connect to the Postgres process: psql -U postgres -d postgres
6. Create the OMOP schema: CREATE SCHEMA omop;
7. Create the tables by running the first DDL: \i OMOPCDM_postgresql_5.4_ddl.sql
8. Load in your vocabulary data to the created tables. For example the concept table: \copy concept FROM 'concept.csv' DELIMITER E'\t' CSV HEADER;

9. Apply the primary keys, constraints, and indexes by running the remaining DDLs:

   • \i OMOPCDM_postgresql_5.4_primary_keys.sql
   • \i OMOPCDM_postgresql_5.4_constraints.sql
   • \i OMOPCDM_postgresql_5.4_indices.sql