Configure Ontology Cell for Installation

As stated in the previous section, there are a couple of files in the edu.harvard.i2b2.ontology directory that will need to be edited to reflect the appropriate configuration at your site. There are several steps that will need to be taken in order to configure the ontology cell for deployment.

Step 1:   Change your working directory

Step 2:   Configure the build properties

Step 3:   Configure the Ontology Application Directory properties

Step 4:   Ontology properties: Set Metadata schema name for the hivedata tables

Step 5:   Ontology properties: Configure PM Cell Properties

Step 6:   Ontology properties: Configure FR Cell Properties

Step 7:   Ontology properties: Configure CRC Cell Properties

Step 8:   Ontology properties: Configure the Ontology service account properties

Step 9:   Ontology properties: Set the metadata delimiter property

Step 10:   Configure the data sources

The configuration files you will be editing are delivered with examples. In some instances these files may contain multiple examples for the three different database management systems supported by the i2b2.


The steps in this section are based on the following assumptions:

Linux: your user has the appropriate administrative access to the opt directory.

Windows: You are logged into the Windows Command Prompt as an Administrator.

If you do not have the appropriate access you will have problems running the scripts.

Step 1: Change working directory

The first step in the cell configuration process is to change your working directory to the location of your edu.harvard.i2b2.ontology folder.

CD YOUR_I2B2_SRC_DIR\edu.harvard.i2b2.ontology


Linux Command:  CD /opt/i2b2/edu.harvard.i2b2.ontology

Windows Command:  CD C:\opt\i2b2\edu.harvard.i2b2.ontology