The R package to upload ATHENA-generated vocabulary csv files into DB

Vocabulary Users
1

It’ not easy to update OMOP vocabulary regularly, because it’s quite burdensome to upload ATHENA-generated vocabulary csv files into the database.

Due to effort of Jun Hyeong Kim, we developed the R package to upload ATHENA-generated vocabulary csv files into DB ,which is now available here.

And please do not upload the vocabulary csv files into existed vocabulary DB, because it will be messed up and lost uniqueness in concept IDs.

Please let us know if you have any problem while using this package.

2

We could put it into the OHDSI Athena or CDM repo? The latter contains a VocabImport folder in each database branch. We could add a generic. Talk to @gregk or @pavgra.

3

Cool, @Christian_Reich Or we’re willing to move this package to OHDSI official github repo. Then we can add some code using this package.
:slight_smile:

Still, this package is somewhat under development, which requires more tests and feedbacks.

4

Just to add to this: in the ETL-Synthea repository there is a script for loading the vocabs from CSV, too. Only for BigQuery its performance may not be overwhelming.