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1.8.
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2 Release Notes
i2b2 1.8.2 Release introduces functionality of userof user-created data table definitions definition and data download of limited data sets (LDS) using the defined data definition. . The data request Management tool enhances the capabilites of the Project manager to manage the data file exports. In addition, there are enhancements to the UI Admin console and UI Query tool and few bug fixes
Highlight of Features
Top New Features
| Description | Modern UI Enhancements with Admin Console | |||
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| Create data table for Export Extension for i2b2 | ||||
| Data Request Manager Extension for i2b2 | ||||
Enhanced Admin Console and UI Query tool | 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 architectures on ORACLE, SQLServer and Postgres databases. | ||
| 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. | |||
| Digital Twin Bundle (distributed separately) |
| Tools for computing loyalty cohorts and computational phenotypes in i2b2. | ||
Bug fixes |
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Community-Contributed Features
Contribution | Contributor | Description | 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 ORACLE, SQLServer and Postgres databases. ||
Detailed Documentation on New Features
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- 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 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
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Additional details on the ontology are available at this link.
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.
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
For historical reference on old 2018 OMOP installation , refer to OMOP Home on i2b2 Community Wiki
Changelog
Database Drivers
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New Features and Improvements
| Web client |
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| Core-server |
CORE-428 Data export Extension for i2b2 using java classes and breakdowns CORE-448 I2b2 on OMOP- Postgres - java changes CORE-450 html injection in Queryname and workplace |
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New Features and Improvements
Bug Fixes
| Core-server / Data | CORE-440 Queries from queue are not processing and returning back||
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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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