1.8.1 Release Notes

i2b2 1.8.0 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
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 architecture 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, 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 ORALE, SQLServer and Postgres databases.

Detailed Documentation on New Features

Data Exporter extension for i2b2

i2b2 Users can now create i2b2 queries using the webclient breakdown Data Request feature. The Options presented in the breadkdown are configurable in the database HIVE_CELL_Params to export a specific data set. Detailed documentation on set up can be at Data Exporter Set-up

Below steps describe the overall process

User logs into i2b2 webclient and creates a regular i2b2 query ,checks the desired Data request breakdown option and selects run query.
Email is sent to the data Manager on the user data request
The manager logs in and rerun the user query by selecting the Data Export breakdown selection to generate the export flat file.
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

Download and extract the newinstall zip package from "Download Binary Distribution" in the top section of https://www.i2b2.org/software
Edit the edu.harvard.i2b2.data\Release_1-8\NewInstall\Metadata\db.properties file to update the project properties to 'ACT' ; db.project=ACT
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
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
Run the scripts to load the Schemes, Table_access and QT_breakdown tables .
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 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

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

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.