About this chapter
The data installation chapter outlines the process of installing the i2b2 data that is specific to the i2b2 on OMOP project. This process involves creating tables, procedures, views as well as loading data into the tables. The i2b2 data being loaded is based off the CMS SynPUF 1k sample data that is provided by OMOP.
In this chapter we will be using the scripts provided in the data package to create tables and load them with sample data.
Assumptions
The data in this package provides data for a domain of i2b2demo and a project of Demo. The assumption is that the PM Service will be configured as such when installing the PM Cell.
Pre-requisites
Before moving forward with the installation of the i2b2 on OMOP tables the following requirements must be met.
The OHDSI maintains the CDM tables, for additional information on setting up these tables, please see the OMOP CDM page.
Requirements Section
Your i2b2 hivedata and pmdata tables have been installed and loaded with the data provided in the standard i2b2 data file. Installed your CDM tables and loaded data from the SynPUF sample data file. CDM tables reside in the same database / schema as your i2b2 tables
TO DO: FINISH THIS NOTE
Note
In your i2b2 database you may or may not have installed the crcdata and metadata tables that are provided in the standard i2b2 data package. If you have installed them you will need to delete them
Order of Installation
It is important the tables, procedures, and views are installed in the order defined below. Failure to do so will result in errors when running the scripts.
CRC Tables
- crcdata: create tables
- crcdata: create procedures
- crcdata: load data
- crcdata: create OMOP views
Ontology Tables
- metadata: create tables
- metadata: load data
Workplace Tables
- workdata: create tables
- workdata: load data
