Downloads:

Documentation:


1.8 Release Notes

i2b2 1.8 Release includes the newly redesigned i2b2 Web interface, ACT i2b2 on OMOP functionality, few improvements and bug fixes.


Highlight of Features

Top New Features

Description

New Web client User Interface


ACT i2b2 on OMOP for MSSQL and Oracle databases


Bug fixes

Community-Contributed Features

Contribution

Contributor

Description

New Web client User Interface

Nick Benik (Harvard Medical School)

The new web client version eliminates usage of YUI, uses the latest versions of jQuery, Bootstrap 5 and Golden-Layout libraries.

ACT i2b2 on OMOP

Michelle Morris (University of Pittsburgh)

Mike Mendis, Jeff Klann, Reeta Metta (Mass General Brigham)

With i2b2 interface, using ACT-OMOP Ontology, queries can be run against OMOP data with OMOP table view structure.  For information on installing and running queries using ACT-OMOP Data model

Detailed Documentation on New Features

New Web client User Interface



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  For historical reference on old 2018 OMOP  installation , refer to OMOP Home - OMOP - i2b2 Community Wiki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 the OMOP metadata and CRC tables and the OMOP Views required to query the OMOP tables.

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 1: Load Ontology tables

  1. Download and extract the new install zip package from "Download Binary Distribution" section of https://www.i2b2.org/software
  2. Edit the  edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata\db.properties file to update the project properties to 'ACT-OMOP'; example: db.project=ACT-OMOP
  3. From the edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata folder, run the ant command: ant -f data_build.xml db_metadata_load_data
    1. This will execute the SQL scripts from the edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata\act\scripts\<db type> folder and will create and load ACT-OMOP Ontology metadata tables. 
  4. You can now verify the new Ontology by logging into the web client.

Step 2: Load OMOP views and Concept dimension

  1. From the edu.harvard.i2b2.data\Release_1-7\NewInstall\Crcdata folder, run the ant command: ant -f data_build.xml db_demodata_load_data
    1. This will execute the  BUILD_ACT_OMOP_Views _<dbtpye> script from the edu.harvard.i2b2.data\Release_1-7\NewInstall\crcdata\act-omop\scripts\<db type> folder and will create the OMOP views under the Views section in the database.
    2. In addition, the corresponding ACT-OMOP concept_dimension data is populated by executing the scripts form the crcdata.zip folders.

              2.  You can now run queries against the OMOP tables from the web client interface

Delete your Patient_dimension and Visit_dimension tables before executing the crc scripts. The OMOP views will build these as Views.

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.

Ontologies derived from visit_dimension or patient_dimension top folders will not have counts because of the way these terms are defined and cannot be rolled up.

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.

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

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 old webclient packaged with default Admin-only configuration


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-33  MSSQL Version of Faster Patient Counting Scripts

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

Bug Fixes

Core-server

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


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.