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The data models of i2b2 and OMOP have many similarities. We take a= dvantage of these similarities to construct an evolution of the i2b2 softwa= re that is able to adapt to the OMOP data model. This adaption = of i2b2 allows the query formulation Application Programming Interface (API= ) to be implemented over an OMOP data source. Therefore, most of the = functionality of i2b2 Software is preserved on OMOP data sources, and as a = result the SHRINE and SMART-on-FHIR tools that rely on the i2b2 API are als= o able to run on the OMOP data model.
The standard i2b2 data model is comprised of a central fact table (obser= vation_fact) surrounded by multiple dimension tables arranged in a star sch= ema. In the Observational Medical Outcomes Partnership Common Data Mo= del (OMOP CDM), rather than a central fact table, we have a collection of t= hem 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.
The i2b2 1.7.09-RC1 software and data packages are designed to= run with OMOP version 5. The sample metadata p= rovided is intended to run queries against the CMS SynPUF 1K d= ata set provided by OMOP. It is recommended that users = of this software are familiar with OMOP and it is required that the synPUF = data is installed.
The i2b2 on OMOP project enables the classic i2b2 Software to run agains= t a database that uses the OMOP CDM (multiple fact tables). This guide alon= g with the provided source code will help configure your system for OMOP CD= M processing.
The i2b2 on OMOP Installation Guide is designed to assist users with installing and setting up an exi=
sting i2b2 environment to work with the OMOP CDM data.
This installation guide assumes the following:
=20 | Important If you are new to i2b2 or = not familiar with how to install and setup the i2b2, we highly recommend yo= u look at the i2b2 Installation Guide and = go through the steps to setup the i2b2 demo environment. | =20
It is important you follow this guide in the order the steps are written= . Some steps need to occur before others in order to prevent issues down th= e road.