Important links
Downloads:
- i2b2 Download Page (binaries and virtual machine): https://www.i2b2.org/software/index.html
- i2b2 - New Web client with redesigned user interface (source code) i2b2/i2b2-webclient: Source code for the i2b2 Web Client (github.com)
- i2b2 GitHub (source code:) i2b2 Foundation (github.com)
Documentation:
- Data Export: Data Exporter (v 1.8.2)
- i2b2-omop install: i2b2-on-OMOP With ENACT-OMOP Ontology v4.1
- totalnum counting scripts: Patient Counting Scripts ("totalnum")
- New Web client and references: New Web Client Install Guide and Help
- Digital Twin Bundle (distributed separately): Digital Twin Technologies
1.8.2 Release Notes
i2b2 1.8.2 Release introduces functionality of user-created data table definition and data download of limited data sets (LDS). The data request Management tool enhances the capabilites of the Project manager to manage the data file exports. In addition, there are enhancements to the UI Admin console and UI Query tool and few bug fixes
Highlight of Features
Top New Features
| Description | ||
|---|---|---|
| Create data table for Export Extension for i2b2 | Create data Table plugin allows the i2b2 User to create their own Data table definitions with desired variables and request data exports using these definiitons. | |
| Data Request Manager Extension for i2b2 | Data Request Manager tool allows an i2b2 Manager to manage and process the User data requests. | |
| Enhance Data Exporter (v1.8.1) | The Data Exporter (v1.81) is enhanced for Manager users to manage and process the exports using the Data Request Manager Console | |
Enhanced Admin Console and UI Query tool | The new webclient has been enhanced with new features such as faster term search, streamlined icons, and an administration console. | |
| Digital Twin Bundle (distributed separately) |
| Tools for computing loyalty cohorts and computational phenotypes in i2b2. |
Bug fixes |
|
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Community-Contributed Features
Contribution | Contributor | Description |
Detailed Documentation on New Features
Data Exporter extension for i2b2
i2b2 data export functionality is now enhanced to empower the i2b2 users to create their own data table definition of desired Ontology variables and make data requests using the User-created table definitions using a patient set query. The workflow involves a new UI console for creating data table definitions and User-created definition breakdowns in the webclient. The Manager user will be able to manage and process the data requests and generate exports. Detailed documentation on set up can be found here: Data Exporter Set-up
The below steps describe the overall process:
- User logs into i2b2 webclient and creates Data table definition using desired Ontology variables
- User runs a regular i2b2 query, checking the desired User-created Data request breakdown option when running the query.
- E-mail is sent to the data manager and the User, informing them that the user's data request has been made.
- The manager logs in and views the data requests using the Data Request Manager Console.
- Manager user generates the data export files using the Data Request Manager Console.
- The generated data file is stored in a configurable location on the i2b2 server.
- An e-mail is sent to the manager confirming the file extract and how to access the files (which can be shared with the requester).
Changelog
Database Drivers
The JDBC drivers were updated to the following versions.
Server Type | oracle | Postgresql | mssql |
|---|---|---|---|
Driver Version | ojdbc8.jar | postgresql-42.7.1.jar | mssql-jdbc-12.4.2.jre8.jar |
Supported Db Server versions
Server Type | SQL Server | Oracle | PostgresSQL |
|---|---|---|---|
Supported Version/s | 2012+ (tested with up to 2022) | 23.3 | 9 to 14 |
Supported software versions
Application Type | Java | Wildfly | Apache HTD | Apache Ant | Apache Axis2 | PHP |
|---|---|---|---|---|---|---|
Supported Version/s | 8 or 11 | 17.0.1Final | 2.0 (RHEL 6) and 2.2 ( RHEL 7) | 1.9.6 | 1.7.1 | 7.2.27 or higher |
Supported Operating Systems
Rocky linux 8 and 9, CentOS versions 7
Windows 2016 -2019
- There is a new PHP install process for IIS in the i2b2 install guide: 2.5.3.2 PHP for Windows
Unofficially, MacOS and other flavors of Linux are likely to work.
i2b2 Server and Client Changes
New Features and Improvements
| Web client |
|---|
WEBCLIENT-368 1.8.2 Webclient update |
| Core-server |
CORE-456 Data Export: agg table CORE-455 Data Export: Request Management admin tool CORE-451 Enhanced Data Export - download file generation CORE-459 updrade to wildfly 34 with axis2 version2 CORE-460 Upgrade to JAVA 17 CORE-454 Upgrade Spring jar to version 6 CORE-447 Update JDBC drivers CORE-458 Software maintainence - drivers, libraries CORE-445 java code folder structure for 1.7 should be changed to refer to 1.8.2 |
i2b2 Database Changes
New Features and Improvements
Bug Fixes
| Core-server / Data | |
|---|---|
ORE-450 html injection in Queryname and workplace CORE-249 Search by code fails ungracefully |
Notes for Developers
For Java 11 install, if you change the xsd (REST API message definitions), then you will need to regenerate gensrc via JAXB in Java 8. In the i2b2-core cell directory for which you're regenerating the XSD-Java, run the ant target "jaxb_gen" on Java 8 and then build as usual using Java 11.
