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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

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. 

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.

Totalnum Scripts Setup

  1. If upgrading, create the totalnum and totalnum_report tables. In Release_1-7/Upgrade/Metadata, run the ant upgrade script.
    ant -f data_build.xml upgrade_tables_release_1-7-12a
  2.  In the Release_1-7/NewInstall/Metadata/ run the ant script to create the stored procedures. 
    ant -f data_build.xml create_metadata_procedures_release_1-7 
  3. Set privileges: If using multiple schemas, the stored procedure should be run from the metadata schema. Make sure the stored procedure can read the tables in the crcdata schema (observation_fact, visit_dimension, patient_dimension) and can both read an update ontology tables in the metadata schema (including table_access). 
  4. If using multiple fact tables, the recommended approach is to create a fact table view as the union of all your fact tables. (This is essentially going back to a single fact table, but it is only used for totalnum counting. This is needed to correctly count patients that mention multiple fact tables within a hierarchy.)
        e.g., 
       create view observation_fact_view as
       select * from CONDITION_VIEW 
       union all
       select * from drug_view
    
If running the counting script in SQL Server, add the wildcard flag, to ignore multifact references in the ontology:
      e.g. exec RunTotalnum 'observation_fact_view','dbo','@','Y'
    This is automatically accounted for in the other database platforms.
Note this approach does not work if you have conflicting concept_cds across fact tables.
  5. Run the stored procedures on your database. This can be done in two ways:


Oracle:     

begin
    RUNTOTALNUM('observation_fact','i2b2demodata');
end; 

You can optionally include a table name if you only want to count one ontology table (this IS case sensitive):
begin
  runtotalnum('observation_fact','i2b2demodata','I2B2');
end;

Note: If you get the error as: ERROR at line 1: ORA-01031: insufficient privilege, then run the command:
        grant create table to (DB USER)  

SQL server: exec RunTotalnum 'observation_fact','dbo','@'
Parameters are: 1) the observation table name (for multi-fact-table setups), 2) the schema name, 3) a single table name to run on a single ontology table or '@' to run on all, and 4) and a wildcard flag that will ignore multifact references in the ontology if 'Y'
PostgreSQL:  select RUNTOTALNUM('observation_fact','public')
Replace 'public' by the schema name for the fact table
If using a schema other than public for metadata, you might need to run "set search_path to 'i2b2metadata','public' " first as well

When finished, verify it is complete by checking that c_totalnum columns in your ontology tables contain numbers (not nulls). These total counts will be visible in the ontology browser in the web client.

Parent folders will get counts (of all patients with facts in the leaves) except for ontology folders derived from visit_dimension or patient_dimension. These cannot be rolled up because of the way these terms are defined in the ontology. They will have no count at all (not a zero).

i2b2 users must have the DATA_AGG user permission to view the counts through the web client.

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.

Driver

ojdbc8.jar

postgresql-42.2.14.jar

mssql-jdbc-9.2.0.jre8.jar

Driver Version

Oracle 21.5

PostgreSQL 42.3.2

MSSql Server 9.2

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.