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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.  Excerpt

Image Removed Requirements Section

:

Image Modified Your i2b2 hivedata and pmdata tables have been installed and loaded with the data provided in the standard i2b2 data file.

Image Modified  Installed your CDM tables and loaded data from the SynPUF sample data file.

The OHDSI maintains the CDM tables, for additional information on setting up these tables, please see the OMOP CDM page.

Image Modified  Your CDM

tables reside in the same database / schema as your i2b2 tables

database or schema have been setup.

Image Added   A database user has been setup.

  • This user is needed to create and load data into the new i2b2 tables.
  • It is also used by the i2b2 Cells when they need to contact the database or schema.
TO DO: FINISH THIS NOTE

 

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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 

 

 

 

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