getting-omop-concept-data

library(omopcept)

omopcept requires OMOP concept tables.

In default operation omopcept will download these concept tables from a temporary online filestore we have created.

You can also download concept tables from Athena and then use omopcept::omop_vocabs_preprocess() to save these in the omopcept package. Note that package results will depend on the subset of vocabularies that you have selected from the Ahena download page.

Details of vocab storage

omopcept by default downloads a selection of vocabularies and stores them locally the first time you use it (in the recommended data location for R packages). The download does not need to be repeated unless you update the package. Vocabularies are stored as parquet files that can be queried in a memory-efficient manner without having to first read the data in to memory.

omopcept::omop_vocab_table_save() is used to save parquet files into the package that we have stored online. You could also use omop_vocab_table_save(from=*) to save vocab parquet files from your own online location.