i2b2 Adaptation to Use Multiple Fact Tables

Allowing software to support OMOP and PCORNet data models

The data models of i2b2 and OMOP have many similarities. We take advantage of these similarities to offer an evolution of the i2b2 software that adapts to the OMOP data model. This allows the query formulation in the i2b2 software that relies on the i2b2 Application Programming Interface (API) to be utilized on top of an OMOP data source. As a result, most of the functionality of i2b2 Software is preserved on an OMOP data source (with proper respect to the OHDSI ontologies). As a result a SHRINE tool or a SMART-on-FHIR tool that relies on the i2b2 API, over OHDSI ontologies, can run with an OMOP data source.


The standard i2b2 data model is comprised of a central fact table (observation_fact) surrounded by multiple dimension tables arranged in a star schema. In the Observational Medical Outcomes Partnership Common Data Model (OMOP CDM), rather than a central fact table, we have a collection of them distinguished by domain: procedures, condition, drug, measurement, observation, etc. In this project, we modify the CRC to run queries against multiple domain fact tables as dictated by the metadata.

This software package is designed to run with OMOP version 5. The sample metadata provided is intended to run queries against the CMS SynPUF 1K data set provided by OMOP (see bottom of page at https://www.ohdsi.org/data-standardization/). It is recommended that users of this software are familiar with OMOP and it is required that the synPUF data is installed.