CommonDataModel
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OHDSI
Can't find the vocabulary loading scripts
Hi friends,
I downloaded the vocabulary 5.0 from athena.ohdsi.org. In the email with the download link, it says:
The control files can be found [here](https://github.com/OHDSI/CommonDataModel). They are provided in the folders Oracle/, PostgreSQL/ and SQL Server/ for the respective SQL dialect. The loading scripts are inside the subfolder VocabImport/.
I am using Postgres and cdm5.4, but I did not see the subfolder of VocabImport in the Postgres folder:
https://github.com/OHDSI/CommonDataModel/tree/master/inst/ddl/5.4/postgresql
Am I going to the wrong place for it?
Thank you for help. Ray
The script can be found on one of the historical branches. https://github.com/OHDSI/CommonDataModel/blob/v5-historical/PostgreSQL/VocabImport/OMOP%20CDM%20vocabulary%20load%20-%20PostgreSQL.sql
@clairblacketer is this script part of the current version of the CommonDataModel package?
We made a decision to not include this with the CDM package as it does not translate well through SqlRender and we felt it made more sense being owned by the vocabulary team. We can bring this up at the next meeting.
@rjiang9 I would also suggest using the ETL-Synthea LoadVocabFromCsv function, or at least the underlying SQL. This is the one I frequently use and it works well in Postgres.
@ablack3 it is not a function in the current package but we can look at adding it. @rjiang9 there is nothing specific for v5.4 that needs to be updated, we just need to add a function to do this.
Thank you for the info @clairblacketer ! I appreciate it. If the email template for the vocabulary down is updated with your 'ETL-Synthea LoadVocabFromCsv function, it will not only remove the confusion but also have a brighter solution. This is no such subfolder with name 'VocabImport' any more.