Using OHDSI tools on UK Biobank Research Analysis Platform (UKB-RAP)

Researchers
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Hi,

Has anyone successfully run OHDSI tooling (e.g., Achilles, CohortMethod) against UK Biobank’s OMOP CDM data on the Research Analysis Platform (RAP)?

As far as I understand, the OMOP tables on RAP are exposed via a Spark-backed database (dxdata/sparklyr, dx xtract_dataset), not a standard RDBMS. DatabaseConnector lists Spark as a supported dbms via JDBC, but I haven’t found confirmation that RAP’s Spark layer exposes an endpoint that external tools can connect to.

So, has anyone gotten DatabaseConnector to connect directly to RAP’s Spark backend? If so, how did you configure the connection? If not, is extract-and-load into a self-hosted Postgres/SQL Server (e.g., via Cloud Workstation) a reasonable workaround (with relation to cost, time), or is there a better-known path?

Thanks

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Update: just heard back from UK Biobank’s Data Analyst Team. The OMOP-format data is no longer available to be added to projects on the UKB-RAP. For more information about why it has been deprecated, restricted and then removed, see here.

Is anyone in the community in touch with UK Biobank about this, working on an updated and improved mapping, or aware of an alternative path to OMOP-formatted UKB EHR data?

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