1.8 Release Notes

i2b2 1.8 Release includes ACT/OMOP V41 Ontology download with easy ANT script install for MSSQL and ORACLE databases, a newly redesigned i2b2 Web interface, and bug fixes.

Highlight of Features

Top New Features

Community-Contributed Features

Detailed Documentation on New Features

ACT Version-4.1 OMOP Ontology data load

ACT V41OMOP metadata and CRC scripts along with OMOP views are now available for load into i2b2 db schema.

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.

Ontology tables load process.

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.

OMOP views and Concept dimension load process

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 data from the webclient

Totalnum counts execution

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.

SAML Authentication

Improved 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:
   • Run the ant command to execute the data_build.xml file with below specified target 
     POSTGRESQL : ant -f data_build.xml db_metadata_run_total_count_postgresql
     ORACLE : ant -f data_build.xml db_metadata_run_total_count_oracle
     SQL SERVER : ant -f data_build.xml db_metadata_run_total_count_sqlserver   
   • Execute the RunTotalNum  stored procedure manually against your database from a SQL Client. This can take several hours for large databases or large ontologies.  Examples are below.

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).

Additional New Stored Procedures

Age In Years Updater

When the CRC data is installed via ant, a new SQL script updates the age_in_years_num in the patient dimension based on the birth dates of the sample patients. As a reminder, this load process can be triggered with ant -f data_build.xml db_demodata_load_data in the CRC directory of NewInstall.

Concept Dimension Updater

Insert_Concept_FROMTableAccess  is designed to populate concept_dimenison table using the ontologies listed in table_access table records.
The stored procedure loops through the table_access  and inserts values from each metadata table (specified in the c_table_name column), when
c_dimtablename is set to 'concept_dimension'
Example usage: exec Insert_Concept_FROMTableAccess

I2b2-Synthea data Load

Synthetic patient data generated by Synthea can be loaded into i2b2. The Synthea SyntheticMass sample files have been converted to i2b2-ACT format, and scripts to load Synthea data from scratch are available here: https://github.com/i2b2/i2b2-synthea

Synthea Load Process

1. Set up an i2b2 project with the ACT ontology.
2. Either download the SyntheticMass 63k sample in i2b2 format from https://github.com/i2b2/i2b2-synthea/blob/main/syntheamass_63K_sample.zip, or follow the instructions below to load any Synthea dataset from scratch. This information can also be found on the Synthea-i2b2 Community Project page.

Loading Synthea data from scratch

1. Download SyntheticMass Data, Version 2 (24 May, 2017) 
   • All data sets (1k, COVID 10k, COVID 100k) have been verified to work EXCEPT the 100k patients in the large SyntheticMass Version 2 download. 
   • The 100k patients in the large SyntheticMass Version 2 download needs an extra step to delete invalid records before import. In this case, download synthea_cleanup.pl to your disk, and then run "synthea_cleanup <directory-for-synthea-csv-files>" The fixed csv files will be in <directory-for-synthea-csv-files>/fixcsv.
2. Set up an i2b2 project with the ACT ontology.
3. Download the scripts from https://github.com/i2b2/i2b2-synthea
4. Run create_synthea_table_<your dbServertype>.sql in your project to create the Synthea tables.
5. Import the Synthea data you downloaded in step one into the Synthea tables in your project.
6. Load the i2b2-to-SNOMED table in this repository into your project. https://www.nlm.nih.gov/healthit/snomedct/us_edition.html
7. Click on the "Download SNOMED-CT to ICD-10-CM Mapping Resources" link to download. (You will need a UMLS account.)
8. Unzip the file
9. Import the TSV file into a table called SNOMED_to_ICD10 in your database.
10. In Postgres and Oracle, follow the additional instructions in the comments at the top of synthea_to_i2b2_<your dbServerType>.sql to clean up the date formatting.
11. Run synthea_to_i2b2_<your dbServertype>.sql to convert Synthea data into i2b2 tables (this will truncate your existing fact and dimension tables!)
12. Replace references to i2b2metadata.dbo in the script. Use the database and schema where your ACT ontology tables are.

ACT Version-4 Ontology data load

Metadata scripts are now available to load the latest ACT Version-4 ontology into your i2b2 db schema.

ACT4 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_1-7\NewInstall\Metadata\db.properties file  to update the project properties to 'ACT' ; db.project=ACT
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 create and load ACT4 Ontology metadata tables 
4. You can now verify the new Ontology  by logging into the webclient.

Security Enhancements

1. i2b2 has been made more secure by addressing parameterization and other potential vulnerabilities found in an internal a Veracode scan.
2. Log4J has been upgraded to the latest version. The following jars are updated in lib/axis2.war/WEB-INF/lib the folder:
   • log4j-api-2.17.1.jar
   • log4j-core-2.17.1.jar
   • log4j-jcl-2.17.1.jar

Improved db Upgrade Process

Previously, i2b2 db upgrade was a multi-step process of running upgrade SQL scripts and stored procedures individually on the db instance. This release simplifies the process of running the table upgrade SQL scripts and stored procedures from data_build.xml files. Details are on the i2b2 Upgrade Page here.

Changelog

Database Drivers

The JDBC drivers were updated to the following versions.

Supported Db Server versions

Supported software versions

Supported Operating Systems

CentOS versions 6 (deprecated) or 7 (highly recommended) 

Windows 7-2019

Unofficially, MacOS and other flavors of Linux are likely to work.

i2b2 Server and Client Changes

New Features and Improvements

i2b2 Database Changes

New Features and Improvements

Bug Fixes

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.