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1.8.
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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 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 . These changes represent a major step forward in i2b2.in 1.8).
Highlight of Features
Top New Features
| Description | ENACT|||
|---|---|---|---|
| Modern UI Enhancements with Admin Console |
| The new webclient has been enhanced with new features such as faster term search, streamlined icons, and an administration console. | |
| Data Exporter extension for i2b2 |
| Using the Run Query breakdown dialog, 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 architectures on ORACLE, SQLServer and Postgres databases. | |
i2b2 on OMOP for MSSQL and Oracle databasesPostgres 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. (MSSQL and Oracle are supported. Postgres support will be added in 1.8.1.) | |
| Digital Twin Bundle (distributed separately) |
| Tools for computing loyalty cohorts and computational phenotypes in i2b2. | |
Bug fixes |
| Bug fixes are included that are needed for OMOP support and for long-running breakdowns. |
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Community-Contributed Features
Contribution | Contributor | Description |
ACT-OMOP design and ontologyOntology Version V4.1 | 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
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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 found here: Data Exporter Set-up
The 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.
- E-mail is sent to the data manager and the User, informing them that the user's data request has been made.
- 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 configurable location on the i2b2 server.
- An e-mail is sent to the manager confirming the file extract and how to access the files (which can be shared with the requester).
Steps to upgrade:
First, install the new war file. Next, upgrade the database. Because the upgrade requires loading some new content from the NewInstall, we have created an ant target to upgrade the data tables: upgrade_tables_release_1-8-0 This should be run from Upgrade/CrcData, e.g., ant f data_build.xml upgrade_tables_1 8-0
Detailed upgrade instructions can be found here: Upgrade to version 1.8.1
ACT - V4.1 Ontology
The V4.1 Ontology includes total of includes 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 ENACT team to get a copy if your institution is an AMA member.
ENACT 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 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 tabledimension
- Run Run the scripts from the edu.harvard.i2b2.data\Release_1-8\NewInstall\Metadata \<dbtype>\scripts folder to load the the Schemes, Table_access and QT_breakdown tables .access tables
- You can now verify the new Ontology by logging into the webclient
Additional details on the ontology are available at this link.
ACT i2b2 on OMOP for
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Postgres database
ACT i2b2 on OMOP functionality uses ACT Ontology in the front-end and enables the i2b2 Software to run against a 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
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enabling use of an OMOP database
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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")
For historical reference on old 2018 OMOP installation , refer to OMOP Home on i2b2 Community Wiki
Changelog
Database Drivers
The JDBC drivers were updated to the following versions.
Server Type | oracle | Postgresql | mssql |
|---|---|---|---|
Driver Version | ojdbc8.jar | postgresql-42.27.141.jar | mssql-jdbc-912.4.2.0.jre8.jar |
Supported Db Server versions
Server Type | SQL Server | Oracle | PostgresSQL |
|---|---|---|---|
Supported Version/s | 2012+ (tested with up to 20192022) | 12g+ and 21c23.3 | 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
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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 fixes/improvements for 1.8.1 |
| Core-server |
CORE-426 running i2b2 on OMOP data model428 Data export Extension for i2b2 using java classes and breakdowns CORE-433 i2b2 on Rocky Linux 9 (CentOS 7 hits EOL 6/2024)448 I2b2 on OMOP- Postgres - java changes CORE-450 html injection in Queryname and workplace |
i2b2 Database Changes
New Features and Improvements
DATA-16 I2b2 17 ACT v4.1 ontology - ANT scripts (github) DATA-24 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 Postgres DATA-38 Loyalty cohort and computational phenotypes stored procedures for MSSQL and ORACLE |
Bug Fixes
| Core-server / Data | |
|---|---|
| CORE-440440 Queries from from queue are not processing and 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.
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