Page History
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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 core support for the OMOP data model on MSSQL and Oracle databases. These changes represent a major step forward in i2b2.
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Top New Features
| Description | |||
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| ENACT Data Exporter | |||
ACT 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 databasesPostgres database |
| The core i2b2 platform now supports the OMOP data model on Postgres database, 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. |
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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. |
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ACT V4.1 Ontology supporting i2b2 and OMOP CDMs enables queries to be run in i2b2 query tool against ORALE, SQLServer and Postgres databases. |
Detailed Documentation on New Features
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ACT - 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.
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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 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 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 table
- Run the scripts to load the Schemes, Table_access and QT_breakdown tables .
- You can now verify the new Ontology by logging into the webclient.
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.
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For historical reference on old 2018 OMOP OMOP installation , refer to OMOP Home on i2b2 Community Wiki
| Info |
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For enabling use of an OMOP database with 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
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New Features and Improvements
| Web client |
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WEBCLIENT-360 New web client User InterfaceWEBCLIENT-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) |
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New Features and Improvements
Bug Fixes
| Core-server / Data |
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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.
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