Developers Getting Started With i2b2
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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.

Change Directory Command
CD YOUR_I2B2_SRC_DIR\edu.harvard.i2b2.ontology


The change directory command shown above is written for Windows. The command itself is the same for both Linux and Windows with the only exceptions being the slashes in the path name and Linux does not include the "drive".

  • Linux Path: use a forward slash.
  • Windows Path: use a backward slash.


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