Important links
Downloads:
- i2b2 Download Page (binaries and (V) 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:
- i2b2-omop install: [DRAFT] i2b2-on-OMOP With ENACT-OMOP Ontology v4.1 - Developers Getting Started With i2b2 - i2b2 Community Wiki
- totalnum counting scripts: Patient Counting Scripts ("totalnum")
- New Web client reference:????
1.8 Release Notes
i2b2 1.8 Release includes the newly redesigned i2b2 Web interface, ACT i2b2 on OMOP functionality, few improvements and bug fixes.
Highlight of Features
Top New Features
| Description | ||
|---|---|---|
New Web client User Interface |
| The completely rewritten web client represents a major step forward for i2b2 that features an improved layout, greater visual customization, and a new plugin architecture. The new web client version eliminates usage of YUI and uses the latest versions of jQuery, Bootstrap 5 and Golden-Layout libraries, which will ensure maintainability far into the future. |
ACT i2b2 on OMOP for MSSQL and Oracle databases | The core i2b2 platform now supports the OMOP data model, which is queryable through the comprehensive ENACT Ontology. (MSSQL and Oracle are supported. Postgres support will be added in 1.8.1.) | |
Bug fixes |
|
.svg.med.png)
Community-Contributed Features
Contribution | Contributor | Description |
| ACT-OMOP ontology | Michelle Morris (University of Pittsburgh) | The ENACT-OMOP Ontology powers the i2b2 queries against OMOP data. (she worked on the views too.) |
Detailed Documentation on New Features
New Web client User Interface
ACT i2b2 on OMOP for MSSQL and Oracle databases
ACT i2b2 on OMOP functionality uses ACT Ontology in the front-end and enables the i2b2 Software to run against a database that uses the OMOP CDM architecture. For historical reference on old 2018 OMOP installation , refer to OMOP Home - OMOP - i2b2 Community Wiki
The following steps will load the OMOP metadata and CRC tables and the OMOP Views required to query the OMOP tables: i2b2-on-OMOP With ENACT-OMOP Ontology v4.1
ACT OMOP Totalnum Scripts
Totalnum Scripts (patient counting scripts) have been updated to improve the counter's performance on both multiple ontology tables and very large(>1.5 million) ontologies such as ACT medications. Debug messages have also been added for troubleshooting and profiling purposes. Support for multiple fact tables has been added and bugfixes have been made.
Patient Counting Scripts ("totalnum")
Improved CRC scripts execution Process
Prior to 1.8 release, CRC scripts via ANT execution command supported single CRC zip folder structure. 1.8 release will support multiple CRV zip folder execution. The databuild.xml has been modified for this process.
Changelog
Database Drivers
The JDBC drivers were updated to the following versions.
Server Type | oracle | Postgresql | mssql |
|---|---|---|---|
Driver Version | ojdbc8.jar | postgresql-42.2.14.jar | mssql-jdbc-9.2.0.jre8.jar |
Supported Db Server versions
Server Type | SQL Server | Oracle | PostgresSQL |
|---|---|---|---|
Supported Version/s | 2012+ (tested with up to 2019) | 12g+ and 21c | 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
Unofficially, MacOS and other flavors of Linux are likely to work.
i2b2 Server and Client Changes
New Features and Improvements
| Web client |
|---|
WEBCLIENT-360 New web client User Interface WEBCLIENT-359 old webclient packaged with default Admin-only configuration |
| Core-server |
|---|
i2b2 Database Changes
New Features and Improvements
DATA-33 MSSQL Version of Faster Patient Counting Scripts DATA-23 Support for multiple crc zip file extraction using databuld.xml DATA-16 I2b2 on OMOP- SQL Server and ORACLE DATA-36 Wrong driver version jdbc 10.2 vs 9.2 in default datasource for MSSQL |
Bug Fixes
| Core-server |
|---|
CORE-440 Queries from queue are not processing and returning back CORE-441 DB Locking issue- can't show previous query when a query is running CORE-442 Get_children doesn't work on Modifier folders CORE-444 Breakdowns for non-Patient_dimension views - don't work CORE-443 Breakdown queueing CORE-445 java code folder structure for 1.7 should be changed to refer to 1.8 CORE-446 php install process on IIS has changed; documentation needs to be updated |
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.
