Introduction

Sharephe is an i2b2 webclient plug-in that improves sharing and translating computable phenotypes for clinical and translational research.

What can Sharephe do?

• Provides user friendly data creation and query tool.
• Structures clinical data into standard query format.
• Uses standardized terminologies and facilitate reuse of value sets.
• Enables shareable, executable and reusable for cross-sites research.
• Support translation among variety of data model (in progress).
• Provides both human readable and computer readable version of phenotypes.

Installation

A guide for installing the Sharephe plug-in in i2b2 webclient.

Prerequisites

• i2b2 Webclient 1.7.13 Release.
• System administrator privileges is needed to install the Sharephe plug-in.

Installing the Plug-in

The following instructions assume that the i2b2 webclient directory is /var/www/html/webclient.

1. Stop the Current Running Services
   • Stop the web server running the i2b2 webclient.
2. Add the Plugin to the i2b2 Webclient
   • Click on the link to download sharephe_plugin.zip.
   • Extract sharephe_plugin.zip file. Once the file has been unzip, there should be a folder called Sharephe.
   • Copy the folder Sharephe, extracted from the sharephe_plugin.zip file, into the i2b2 webclient plugin directory /var/www/html/webclient/js-i2b2/cells/plugins/community.
3. Configure the i2b2 Webclient
   • Add the following code to the array i2b2.hive.tempCellsList in the module loader configuration file i2b2_loader.js located in the directory /var/www/html/webclient/js-i2b2:

     {code: "Sharephe",
         forceLoading: true,
         forceConfigMsg: {params: []},
         roles: [ "DATA_LDS", "DATA_DEID", "DATA_PROT" ],
         forceDir: "cells/plugins/community"
     }                                        

     Remember to make a backup copy of the file before modifying it.
     For an example, the i2b2_loader.js file should look similar to this:

     i2b2.hive.tempCellsList = [
         {code: "PM",
             forceLoading: true 			// <----- this must be set to true for the PM cell!
         },
         {code: "ONT"},
         {code: "CRC"},
         {code: "WORK"},
         {code: "Sharephe",
             forceLoading: true,
             forceConfigMsg: {params: []},
             roles: [ "DATA_LDS", "DATA_DEID", "DATA_PROT" ],
             forceDir: "cells/plugins/community"
         },
         ...
     ];

     For more information on installing the plug-in, please visit Web Client Plug-in Developers Guide.
4. Restart the Services
   • Restart the web server running the i2b2 webclient.

Configuring the Plug-in

Setting the REST API URL

Set the value for i2b2.Sharephe.rest.url in the file Sharephe_rest_services.js located in the directory /var/www/html/webclient/js-i2b2/cells/plugins/community/Sharephe to the following URL:

https://sharephe.dbmi.pitt.edu/api

For an example:

i2b2.Sharephe.rest.url = 'https://dev.sharephe.dbmi.pitt.edu/api';