PREVIEW VERSION AVAILABLE NOW. FINAL VERSION WILL BE RELEASED IN DECEMBER 2023.

Design

Utilizing i2b2's reusable application programming interface (API)  to support OMOP data model. The ACT-OMOP ontology queries OMOP table views that correspond to the OMOP table structure. On one database, the OMOP data and the i2b2 application layer are loaded. With the ontology, it becomes possible to query OMOP tables using the i2b2 interface. The design document can be found here.

Step 1: Acquire downloads

First, download the necessary components onto a computer that can connect to your target database and from which you can run SQL queries.

• Download i2b2.
  • Download and extract the newinstall zip package from "Download Binary Distribution" in the top section of  https://www.i2b2.org/software
  • Determine if you need to install any additional required packages, such as Java JDK or Ant: Chapter 2. Requirements
  • If running less than i2b2 1.8, separately download the latest data package from GitHub https://github.com/i2b2/i2b2-data to get the ACT-OMOP ontologies. 
• OMOP 5.4 DDL SQL Scripts: https://github.com/OHDSI/CommonDataModel/tree/main/inst/ddl/5.4
  • Either clone the repository or download the ETL scripts for your database platform.

Step 2: Create core tables and Views (OMOP, i2b2, and ACT-OMOP specific):

• OMOP: If you will be creating a new OMOP database for this installation, then:
  • Run the OMOP 5.4 DDL SQL Scripts you downloaded in the last step, using a SQL client.
    
    • It is recommended to run the DDL, indices, and primary key scripts, but NOT the constraints scripts. This can cause problems during ETL.
• If you have not installed i2b2 previously (i.e. you are not setting this up as an i2b2 Project in a larger installation):
  • 3.5 Hivedata Tables
  • 3.8 PM Table
• Make sure i2b2 is configured for multiple fact tables by changing the appropriate entry in the database.
  • 3.11 Multiple Fact Tables

• i2b2: Follow the instructions in Chapter 3 of the i2b2 installation guide to create the additional i2b2 tables needed for the application server: Chapter 3. Data Installation, these sections specifically:
• 3.4 Crcdata Tables
  • In 3.4.2, edit the CRC db properties file to set db.project parameter  to act-omop.             
    
  • Perform step 3.4.3-3.4.5 and drop/rename the PATIENT and VISIT_DIMENSION tables. E.g., run the commands:

                               ant -f data_build.xml create_crcdata_tables_release_1-7 

FROM THE DATABASE: DROP PATIENT_DIMENSION; DROP VISIT_DIMENSION;

ant -f data_build.xml create_procedures_release_1-7

ant -f data_build.xml db_demodata_load_data

The final ant script will create act-omop Views, which point to the OMOP tables, and loads the concept_dimension table with act-omop concepts data, as well as creating the standard CRC tables and procedures.

Step 3: ACT-OMOP v4 ontology data load process

• Follow the instructions in Chapter 3 of the i2b2 installation guide to create and load the ACT-OMOP metadata project.
• 3.7 Metadata Tables
  • In 3.7.2, edit the Metadata db properties file.  In db.properties, set db.project=ACT-OMOP  parameter which will direct the ant script to load the ACT-OMOP ontology.                          
  • In 3.7.4, only load the regular data, not the identified data. 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_1-7\NewInstall\Metadata\act-omop\scripts\<db type> folder and:
    • Creates ACT-OMOP v4 Ontology metadata tables with indexes. 
    • Loads the act-omop metadata

Step 4: Create Project

Finally set up an i2b2 OMOP project pointing to the i2b2-OMOP database that you just configured.  

6.6.0. [DRAFT] Guide to creating a new project with the admin tool.

Verify the Ontology is displayed and queriable from the webclient

Notes

Both the ACT-OMOP Ontology tables, views and data is available under edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata\act-omop folder.

The scripts are in this folder:

These are the ACT-OMOP ontology tables.

These are the ACT-OMOP views:

• ETL OMOP data
• This is a site-specific process, but OHDSI's WhiteRabbit tool can help: https://github.com/OHDSI/WhiteRabbit