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Assumptions
- The data in this package
- is based on the CMS SynPUF 1K data set provided by OMOP.
- The project for this installation will be called omop.
- The PM Cell and hive are already installed.
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<img src="https://community.i2b2.org/wiki/download/attachments/14091764/icon_note.png" width="16" height="16" align="absmiddle" alt="info" border="0">
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<b>Note</b>
<br><br>You will need to know the domain that was defined during the PM Cell installation.
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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 stored procedures
crcdata: load data
crcdata: create OMOP views
Ontology Tables
metadata: create tables
metadata: load data data
Workplace Tables
workdata: create tables
workdata: load data
Extract the i2b2 Data Package
In the Requirements Chapter of this install document you downloaded a zip file that contained the i2b2 on OMOP data package. This zip file contains only those data installation scripts needed to create the i2b2 tables and load sample data for this project.
Steps to extract the code
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1. Set up a target source directory for the i2b2 on omop data. |
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2. Locate the i2b2_omop_data.zip file you downloaded in the Requirements chapter. |
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3. Extract the data package into the target source directory you just created. |
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You will want to make note of the location as it will be needed further along in the i2b2 installation. In the installation document whenever you see YOUR_I2B2_DATA_DIR it will need to be replaced with the location of your i2b2 Data files. For your convenience an installation Worksheet to track the setup locations has been provided in the Appendices Chapter of the i2b2 Installation Guide.. |
Directory Structure and Schema Mapping
workdata: load data
