THIS FEATURE WILL BE AVAILABLE MARCH 2023

Objective

 Utilize the concept of a reusable application programming interface (API)  by using i2b2 API to adapt and support OMOP data model. Below steps involve creating datamodel-specific i2b2 ontologies and mapping these to query non-standard OMOP table structure

Steps to build ACT-OMOP Ontology

Step1: Create OMOP tables and load data using:

•  OMOP 5.4 DDL SQL Scripts: https://github.com/OHDSI/CommonDataModel/tree/main/inst/ddl/5.4
• It is recommended to run the DDL, indices, and primary key scripts, but NOT the constraints scripts. It can cause problems during ETL.
• ETL OMOP data
• This is a site-specific process, but OHDSI's WhiteRabbit tool can help: https://github.com/OHDSI/WhiteRabbit

Step 2: Create ACT-OMOP CRC and  i2b2 core tables (e.g., QT and breakdowns) 

• Download i2b2. (Download and extract the newinstall zip package from "Download Binary Distribution" in the top section of  https://www.i2b2.org/software)
• 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 with  ACT-OMOP  project parameter which will be used to build the concept_dimension table from metadata tables later in the process.                             
  •        Skip section 3.4.5 for now.    

• 3.5 Hivedata Tables
• 3.8 PM Tables

Step 3: ACT-OMOP v4 ontology data load and Views creation process

• Follow the instructions in Chapter 3 of the i2b2 installation guide to load the ACT-OMOP metadata project.
• 3.7 Metadata Tables
• • In 3.7.2, edit the Metadata db properties file with  ACT-OMOP  project parameter which will direct the ant script to load the ACT-OMOP ontology. In db.properties, set db.project=ACT-OMOP                             
  • In 3.7.3, do they skip CREATE METADATA????
  • 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. This will:
    • Create and load ACT-OMOP v4 Ontology metadata tables with indexes. 
    • Create the ACT-OMOP views by executing BUILD_ACT_OMOP_VIEWS_ALL_MSSQL.sql

Step 4: Build ACT-OMOP CONCEPT DIMENSION

Perform step 3.4.5. This must be done after the metadata are loaded. From the edu.harvard.i2b2.data\Release_1-7\NewInstall\CRC folder, run the ant command: ant -f data_build.xml db_demodata_load_data

This will execute the create_omop_act_concept_dimension SQL script from the edu.harvard.i2b2.data\Release_1-7\NewInstall\Crcdata\scripts\act-omop\<db type> folder and loads A concept dimension table

Step 5: 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: