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1.8.0 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

ENACT 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 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. 

Community-Contributed Features

Contribution

Contributor

Description

ACT-OMOP design and ontology

Michele Morris (University of Pittsburgh)

The ENACT-OMOP Ontology powers the i2b2 queries against OMOP data, 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

ENACT - 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.

ENACT 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 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. 

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


ACT OMOP Totalnum Scripts

Totalnum Scripts (patient counting scripts) have been updated with bugfixes, and the MSSQL version has been rewritten and is 5x faster. 

Patient Counting Scripts ("totalnum")

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)

1.9.61.7.17.2.27 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

WEBCLIENT-360 New web client User Interface

WEBCLIENT-359 classic webclient - configurable for Admin functionality                                                                                                                                                                                                                                                                

Core-server

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

DATA-16 I2b2 on OMOP- SQL Server and ORACLE                                        

DATA-23 Support for multiple crc zip file extraction using databuld.xml 

DATA-33  MSSQL Version of Faster Patient Counting Scripts                                                                                                                                                                                                                                                                                                

Bug Fixes

Core-server / Data

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.