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Downloads:

Documentation:

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

Data Exporter extension for i2b2

Using the webclient breakdowns, 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. 

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 at Data Exporter Set-up

Below steps describe the overall process

  • User logs into i2b2 webclient and runs a regular i2b2 query, checking the desired Data request breakdown option when running the query.
  • An e-mail is sent to the data manager on the user data request
  • 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 location specified in the HIVE_CELL_Params setting.
  • Email is sent to the user confirming the file extract and how to access the files.

ACT - V4.1 Ontology

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

See ENACT Version 4.1 info for installation instructions.

Metadata and CRC zip files are provided to load the latest ENACT Version-4.1 ontology into your db schema using ANT scripts.

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.

ACT V4.1 data load process

  1. Download and extract the newinstall zip package from "Download Binary Distribution" in the top section of https://www.i2b2.org/software
  2. Edit the  edu.harvard.i2b2.data\Release_1-8\NewInstall\Metadata\db.properties file  to update the project properties to 'ACT' ; db.project=ACT
  3. From the edu.harvard.i2b2.data\Release_1-8\NewInstall\Metadata folder, run the ant command: ant -f data_build.xml db_metadata_load_data.This will execute the SQL scripts from the edu.harvard.i2b2.data\Release_1-8NewInstall\Metadata\act\scripts\<db type> folder to create and load the metadata tables 
  4. From the edu.harvard.i2b2.data\Release_1-8\NewInstall\crcdata folder, run the ant command: ant -f data_build.xml db_demodata_load_data.This will execute the SQL scripts from the edu.harvard.i2b2.data\Release_1-8NewInstall\crcdata\act\scripts\<db type> folder to create and load the concept_dimension table
  5. Run the scripts to load the  Schemes, Table_access and QT_breakdown tables .
  6. You can now verify the new Ontology by logging into the webclient.


ACT i2b2 on OMOP for Postgres database

ACT i2b2 on OMOP functionality uses ACT Ontology in the front-end and enables the i2b2 Software to run against Postgres database that uses the OMOP CDM architecture. 

Documentation on loading the OMOP metadata, CRC tables, and CRC OMOP Views required to query the OMOP tables can be found here: i2b2-on-OMOP With ENACT-OMOP Ontology v4.1

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

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



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 2022)

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)

1.9.61.7.17.2.27 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

                                                                                                                                                                                                                                                        

Core-server

                                                                                                                                                                                                                                                                                                             

i2b2 Database Changes

New Features and Improvements

                                                                                                                                                                                                                                                                                       

Bug Fixes

Core-server / Data



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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