PIONEER OMOP repository

Contents:

• OMOP CDM definition plus extensions
• Data loading scripts
• PIONEER vocabulary extension

Data loading process

As implemented in load_cdm_data.ipynb

Inputs:

• cdm schema name
• results schema name

1. CREATE SCHEMA <schema_name>;
2. SET search_path TO <schema_name>;
3. pioneer_omop_cdm/OMOP CDM postgresql v6_0_dev ddl.sql
4. load data
5. pioneer_omop_cdm/OMOP CDM postgresql v6_0_dev constraints.sql
6. pioneer_omop_cdm/OMOP CDM postgresql v6_0_dev pk indexes.sql
7. other/vocab_view.sql
8. CREATE SCHEMA <results_schema_name>;
9. SET search_path TO <results_schema_name>;
10. other/results_ddl_hierarchy_2.7.4.sql
11. Run Achilles in R
12. Add new source in Atlas Configuration via configuration UI