Database specific thread: postgres

Vojtech_Huser · March 8, 2019, 10:05pm

Our team at NLM recently created some code and guidance around creating OMOP tables and loading vocab. We also will be loading demo data.

I wanted to share our experience (and some code) as we did that.
If there are other postgres users, it would be nice to learn from each other what works and what is challenging.

Our empty OMOP database setup is here.

github.com

Sigfried/ohdsi_pg_setup/blob/master/empty_omop.md

Setting up an empty OMOP CDM
================
Sigfried Gold
February 28, 2019

For a PostgreSQL database
-------------------------

### CDM and vocabulary files

These instructions assume you already have postgres DDL and related files from <https://github.com/OHDSI/CommonDataModel>. We only need files from the PostgreSQL directory:

``` bash
./CommonDataModel/PostgreSQL/OMOP CDM postgresql constraints.txt
./CommonDataModel/PostgreSQL/OMOP CDM postgresql ddl.txt
./CommonDataModel/PostgreSQL/OMOP CDM postgresql pk indexes.txt
./CommonDataModel/PostgreSQL/README.md
./CommonDataModel/PostgreSQL/VocabImport
./CommonDataModel/PostgreSQL/VocabImport/OMOP CDM vocabulary load - PostgreSQL.sql
./CommonDataModel/PostgreSQL/OMOP CDM Results postgresql ddl.txt

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(credit goes to Sigfried Gold)