Downloads:

Relevant Documentation:


1.8.2-beta Release Notes

i2b2 1.8.2-beta Release introduces functionality of user-created data table definition and data download of limited data sets (LDS). The Data Request Management tool enables project managers to manage the data file exports. In addition, there are minor improvements in the Query tool, improvements to the fast "totalnum" patient counting scripts,  and some bug fixes.

Highlight of Features

Top New Features

Description

Create data table for Export Extension for i2b2

The Create Data Table tool allows the i2b2 user to create their own data table definitions with ontology variables and then request data exports in the Run Query dialog.

Data Request Manager Extension for i2b2

The Data Request Manager tool allows an i2b2 manager to manage and process the user data requests. 


NOTE: In this beta release, clicking Create File on a custom-table data request in a Postgres database does not actually generate the file.

Enhanced Data Exporter (v1.8.1)

v1.8.1-style data exports (pre-defined tables defined by domain) can now be run and managed using the new tools. Manager users can manage and generate these data file exports using the Data Request Manager Console

ENACT Ontology v4.2

Upgraded to UMLS 2025AA:

  • Lab (Provisional)
  • Medications grouped alphabetically
  • Medications grouped by VA Classification
  • Diagnosis ICD10CM
  • Procedures CPT4
  • Procedures HCPCS
  • Procedures ICD10PCS

Other updates:

  • Lab (Common)
  • Demographics
  • Social Determinants of Health
  • Research Ontology
  • Vaccines

 Update to new secure versions of software


The new server uses Java 17, Wildfly 37.01, and Axis2 v2

Digital Twin Bundle (distributed separately) 

Tools for computing loyalty cohorts and computational phenotypes in i2b2. 

Bug fixes


Detailed Documentation on New Features

Data Exporter extension for i2b2

i2b2 data exporter functionality is now enhanced the enable i2b2 users to create their own Data table definitions  from ontology elements. The data table definitions are displayed as options that can be selected in the Run Query dialog. Users can submit multiple data requests for with a query.  The Manager user can manage the data requests and generate data files using a Data Request Manager console.  Detailed documentation on set up can be found here: Data Exporter Set-up

The below steps describe the overall process:

ACT - V4.1 Ontology

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

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 ENACT 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 
  5.  Run the scripts from the edu.harvard.i2b2.data\Release_1-8\NewInstall\Metadata \<dbtype>\scripts folder to load the Schemes, Table_access tables
  6. You can now verify the new Ontology by logging into the webclient

Additional details on the ontology are available at this link.

ACT Fast Totalnum Scripts

The 5x faster totalnum scripts (patient counting scripts) are now available for all three database platforms!

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-42.7.1.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

11 to 14 (9 and 10 work for querying, but not data export)

Supported software versions

Application Type

Java

Wildfly

Apache HTD

Apache Ant

Apache Axis2

PHP                                           

Supported Version/s

17

37.01

2.0 (RHEL 6) and 2.2 ( RHEL 7)

1.9.627.2.27 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-368   1.8.2 Webclient update                                                                                                                                                                                                                      

Core-server

CORE-456 Data Export: agg table

CORE-455  Data Export: Request Management admin tool

CORE-451 Enhanced Data Export - download file generation

CORE-459 updrade to wildfly 34 with axis2 version2

CORE-460 Upgrade to JAVA 17

CORE-454 Upgrade Spring jar to version 6

CORE-447  Update JDBC drivers

CORE-458 Software maintainence - drivers, libraries

CORE-445  java code folder structure for 1.7 should be changed to refer to 1.8.2                                                                                                                                                                                                                                                    

i2b2 Database Changes

New Features and Improvements

DATA-51     RPDO custom table export stored procedures    

DATA-51     Data exporter (v1.8.2) - Add RPDO_Table_Request and Qt_breakdown_path change- add column       

DATA-32     Faster Totalnum (patient counting) script!                                                                                                                                                                                                

Bug Fixes

Core-server / Data

CORE-450 html injection in Queryname and workplace

CORE-249 Search by code fails ungracefully



Notes for Developers

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 17.