I3PO README
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The Integrated Informatics Interface for Processing the Ontology (I3PO) is an addition to the I2B2 framework allowing for dictionary-like lookup of definitions for terms in the I2B2 ontology. It is packaged as a cell/webclient-plugin combination, and both components are necessary for its usage.

These instructions assume that I3PO will be run in Apache Tomcat on a *nix-based operating system (tested on Ubuntu 10.04 & 10.10); deployment in another servlet container, while possible, is not covered in this document and requires additional steps specific to the container. Commands in the deploy.sh file can be easily adapted to your operating system of choice.


Required Software
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- Java JDK
	5.0 or higher is required; skip this if already installed

	1. Download JDK from http://www.oracle.com/technetwork/java/javase/downloads/index.html or from
		your system's pakage manager.  
	2. Install the JDK into directory of your choice if you didn't use a package manager.
	3. Set  $JAVA_HOME  environment  variable  to  point  to  the  installation  directory  (e.g., 
		/usr/lib/jvm/java-1.6.0-openjdk).
	4. Add $JAVA_HOME/bin to your PATH variable in your .bashrc or /etc/environment file (e.g., 
		export PATH=$PATH:$JAVA_HOME/bin).

- UMLS
	The DEF Cell relies on the UMLS database for definition mapping. UMLS requires users to 
	obtain a usage license.  Please obtain a UMLS license at http://umlsks.nlm.nih.gov.

	1. Download files from http://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html
	2.