ETL & Mapping Guidance

What is ETL to the OMOP CDM?

Extract, Transform, Load (ETL) is the process of converting your source data — typically from an electronic health record (EHR) or other clinical system — into the OMOP Common Data Model (CDM). A well-designed ETL maps both the structure of your source data (which table/column a fact belongs in) and the content of your source data (which standard vocabulary concept a local code represents).

This section covers the parts of that process that are specific to health systems: working with EHR source systems, mapping local terminologies to OMOP standard vocabularies, and the data governance responsibilities that come with handling clinical data.

Start here

• Book of OHDSI — the primary reference text for the OHDSI community and the OMOP CDM. Read the ETL chapters before starting a new mapping project.

• OHDSI ETL Tutorial — walkthrough materials for building an ETL pipeline to the OMOP CDM.

• EHDEN Academy — free online courses covering OMOP CDM, vocabulary mapping, and OHDSI tools.

In this section

• EHR Source Systems — guidance specific to extracting data from your EHR.

• Terminology & Vocabulary Mapping — mapping local/interface terminologies to OMOP standard concepts.

• Data Governance — proprietary data and PHI considerations for ETL work.

See the Resources page for the full list of OHDSI tools referenced throughout this section.