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Documentation:
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1.8.0 Release Notes
i2b2 1.8 Release includes the newly redesigned i2b2 Web interface, ACT i2b2 on OMOP functionality, few improvements and bug fixes..0 Release introduces two major improvements to the platform that enhance usability and applicability: a redesigned and completely rewritten i2b2 Web Interface to improve the user experience, and core support for the OMOP data model on MSSQL and Oracle databases. These changes represent a major step forward in i2b2.
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. |
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-OMOP Ontology. (MSSQL and Oracle are supported. Postgres support will be added in 1.8.1.) |
Bug fixes |
| Bug fixes are included that are needed for OMOP support and for long-running breakdowns. |
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Community-Contributed Features
Contribution | Contributor | Description |
ACT-OMOP design and ontology | Michelle Michele Morris (University of Pittsburgh) | The ENACT-OMOP Ontology powers the i2b2 queries against OMOP data . (she worked on the views too.), and the design of the database views enables the queries to run. |
1.8.1 will be released In April 2024 and will add Postgres support for OMOP, Snowflake database support, SQL job scheduling, and improved data export.
Detailed Documentation on New Features
New Web client User Interface
The new Web Client modernizes the i2b2 query tool, and features:
- Removal of antiquated support libraries.
- Creation of new compartmentalized plugin execution environment with support for legacy plugins.
- Drag and Drop system reworked to use browser-native operations.
See i2b2 Web Client Install for installation instructions.
The Admin functionality is still supported through the classic web client. See i2b2 Administration Module Install for more information. In particular, pay attention to the configuration file change in 6.4 Configuration which enables an admin-only version of the classic webclient.
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
Documentation on loading the OMOP metadata and , CRC tables, and the CRC OMOP Views required to query the OMOP tables can be found here: i2b2-on-OMOP With ENACT-OMOP Ontology v4.1
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The CPT4 ontology table is not included with i2b2 due to AMA restrictions on redistribution of CPT code information. Contact the ACT team to get a copy if your institution is an AMA member. |
Step 3: Execute Totalnum counts
Load and execute file totalnum_usp/sqlserver/totalnum_fast_prep_OMOP.sql and run the following command:
exec totalnum_fast_prep_OMOP 'observation_fact','dbo','@
When finished, verify by checking that c_totalnum columns in your ontology tables contain numbers. These total counts will be visible in the ontology browser in the web client for 2b2 users with DATA_AGG user permission.
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For historical reference on old 2018 OMOP installation , refer to OMOP Home on i2b2 Community Wiki
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For enabling use of an OMOP database with i2b2, follow the instructions in the install guide for a new install of i2b2 using the i2b2-OMOP install option. The documentation here will guide you through this process. 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.with bugfixes, and the MSSQL version has been rewritten and is 5x faster.
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 |
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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 |
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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 |
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| 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 |
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WEBCLIENT-360 New web client User Interface |
classic webclient - configurable for Admin functionality |
| Core-server |
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CORE-426 running i2b2 on OMOP data model CORE-433 i2b2 on Rocky Linux 9 (CentOS 7 hits EOL 6/2024) |
i2b2 Database Changes
New Features and Improvements
xml DATA-33 MSSQL Version of Faster Patient Counting Scripts |
Bug Fixes
| Core-server / Data |
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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 update |
| DATA-36 Wrong driver version jdbc 10.2 vs 9.2 in default datasource for MSSQL |
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.
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