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1.8.1 Release Notes

i2b2 1.8.1 Release builds on the rewritten web interface introduced in 1.8 with new features and new administration tools, it introduces a powerful new data export module, and it adds core support for the OMOP data model on Postgres databases (adding to MSSQL and Oracle databases in 1.8). 

Highlight of Features

Top New Features

Description

Modern UI Enhancements with Admin Console

The new webclient has been enhanced with new features such as faster term search, streamlined icons, and an administration console.
Data Exporter extension for i2b2

Using the Run Query breakdown dialog, patient data can be exported as flat files to be loaded into SAS, R and other data analytic tools for further analysis.

ACT Ontology Version 4.1

Version 4.1 provides 19 ontologies supporting i2b2 and OMOP CDM architectures on ORACLE, SQLServer and Postgres databases.

i2b2 on OMOP for Postgres database

The core i2b2 platform now supports the OMOP data model on Postgres database (adding to existing Oracle and SQLServer OMOP support), which is queryable through the comprehensive ENACT-OMOP Ontology. 

Digital Twin Bundle (distributed separately) 

Tools for computing loyalty cohorts and computational phenotypes in i2b2. 

Bug fixes


Community-Contributed Features

Contribution

Contributor

Description

ACT-Ontology Version V4.1

Michele Morris (University of Pittsburgh)

The ACT V4.1 Ontology supporting i2b2 and OMOP CDMs enables queries to be run in i2b2 query tool against ORACLE, SQLServer and Postgres databases. 

Detailed Documentation on New Features

Data Exporter extension for i2b2

i2b2 can now export patient data for a patient set. The workflow involves breakdowns in the webclient, which allow users to request exports and data managers to generate exports. The export types and options are fully configurable in the database. Detailed documentation on set up can be found here: Data Exporter Set-up

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  • User logs into i2b2 webclient and runs a regular i2b2 query, checking the desired 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 reruns the user query with the Data Export breakdown selection to generate the export flat files.
  • The generated export flat 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).

Steps to upgrade:

First, install the new war file. Next, upgrade the database. Because the upgrade requires loading some new content from the NewInstall, we have created an ant target to upgrade the data tables: upgrade_tables_release_1-8-0 This should be run from Upgrade/CrcData, e.g., ant f data_build.xml upgrade_tables_1 8-0 

Detailed upgrade instructions can be found here: Upgrade to version 1.8.1

ACT - V4.1 Ontology

The V4.1 Ontology includes  19 ontologies- 3 new and 11 updated and 5 unchanged

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For historical reference on old 2018 OMOP installation , refer to OMOP Home on i2b2 Community Wiki

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)

1.9.61.7.17.2.27 or higher                                              

Supported Operating Systems

 Rocky linux 8 and 9, CentOS versions  7

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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 fixes/improvements for 1.8.1                                                                                                                                                                                                                                                 

Core-server

CORE-428  Data export Extension for i2b2 using java classes and breakdowns

CORE-448  I2b2 on OMOP- Postgres - java changes             

CORE-447 Update JDBC drivers   

CORE-450 html injection in Queryname and workplace                                                                                                                                                                                                                                                                

i2b2 Database Changes

New Features and Improvements

DATA-17   ACT v4.1 ontology - ANT scripts (github)

DATA-24  I2b2 on OMOP- Postgres  

DATA-38  Loyalty cohort and computational phenotypes stored procedures for MSSQL and ORACLE         

 DATA-32  Faster Totalnum (patient counting) script!                                                                                                                                                                                                                                    

Bug Fixes

Core-server / Data
CORE-440  Queries from queue are not processing and returning back   


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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