Bigquery schemas for CDM 5

Javier · May 19, 2020, 8:30am

Hello,

We would like to load the CDM v5 into BigQuery, however on the github repo (https://github.com/OHDSI/CommonDataModel/tree/master/BigQuery) these schemas are only available for CDM v6.

Since v5 is the more commonly used, has any one writen the BigQuery for CDMv5 ??

thanos_vidakis · May 19, 2020, 8:34am

Not sure if this is the correct answer as I am new here but you might try to check code from the tag v5.3.1

github.com

OHDSI/CommonDataModel/blob/v5.3.1/BigQuery/OMOP CDM bigquery ddl.txt

/*OMOP CDM v5.3.1 14June2018*/
#standardsql
create table concept (
  concept_id			    INT64			  not null ,
  concept_name			  STRING     	not null ,
  domain_id				    STRING   		not null ,
  vocabulary_id			  STRING   		not null ,
  concept_class_id		STRING  		not null ,
  standard_concept		STRING  		         ,
  concept_code			  STRING  		not null ,
  valid_start_DATE		DATE			  not null ,
  valid_end_DATE		  DATE			  not null ,
  invalid_reason		  STRING
)
;


create table vocabulary (
  vocabulary_id			    STRING   		not null,
  vocabulary_name		    STRING     	not null,

This file has been truncated. show original

Hope this is helpful

Javier · May 19, 2020, 8:40am

Ok, thanks a lot @thanos_vidakis .
I had selected 5.3.2 and they did not appear there. I thougth they did not existed before that point.

gregk · May 19, 2020, 12:43pm

@Javier I do not believe there is 5.3.2 release (yet). The latest is 5.3.1 - please pick this one

mgkahn · May 20, 2020, 7:29pm

The is the GBQ DDL for 5.3.1 that we use at the University of Colorado. I did not attempt to do a diff with what Gregory posted.

OMOP V5.3.1 BigQuery DDL.docx (23.6 KB)