Thank you for your effort in making this sample dataset. It is really helpful for someone like me who is new to OHDSI. I still have a few questions about setting up the cdm schema and wonder if you or someone else could help me out.
I followed the link in the readme (https://github.com/OHDSI/CommonDataModel/tree/v5.2.2) to create an empty cdm schema:
execute the script OMOP CDM ddl - PostgreSQL.sql to create the tables and fields, which generates 37 tables under cdm schema
load the data into the schema using the 18 csv files in the sample dataset
then I ran the script OMOP CDM constraints - PostgreSQL.sql to add the constraints. However, I encountered a lot of errors when running this script, for example, here is one of the error:
ERROR: insert or update on table “person” violates foreign key constraint “fpk_person_gender_concept”
DETAIL: Key (gender_concept_id)=(8507) is not present in table “concept”.
I think this is caused by the concept table which is currently empty. And I found that in the link mentioned above, there is an extra step to load CMD vocabulary, which seems to populate the concept table.
So, my question is where can I find the CMD vocabulary csv files?
Thank you for the help!