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

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 i2b2 core tables (e.g., QT and breakdowns)

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
- Skip 3.4.5, which loads the i2b2 demo data.
3.5 Hivedata Tables
3.8 PM Tables

Step 3:ACT-OMOP v4 ontology data load process

Download i2b2. (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_1-7\NewInstall\Metadata\db.properties file to update the project properties to 'ACT_OMOP' ; db.project=ACT_OMOP
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

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 ACT-OMOP v4 Ontology metadata tables with indexes. You can now verify the new Ontology by logging into the webclient.

This creates these tables;

ACT_ICD10CM_DX_V4_OMOP

ACT_ICD10PCS_PX_V4_OMOP

ACT_ICD9CM_DX_V4_OMOP

ACT_ICD9CM_PX_V4_OMOP

ACT_CPT4_PX_V4_OMOP

ACT_HCPCS_PX_V4_OMOP

ACT_MED_ALPHA_V4_OMOP

ACT_MED_VA_V4_OMOP

ACT_LOINC_LAB_PROV_V4_OMOP

ACT_SDOH_V4_OMOP

ACT_VITAL_SIGNS_V4_OMOP

ACT_VISIT_DETAILS_V4_OMOP

ACT_COVID_V4_OMOP

ACT_DEM_V4_OMOP

ACT_ICD10_ICD9_DX_V4_OMOP

Step 4: Create OMOP views.

In the CRC database, create the views needed for the ontology to access the OMOP tables. Run BUILD_ACT_OMOP_VIEWS_ALL_MSSQL.sql for the sql db instance. This will create following views:

CONDITION_VIEW;

DRUG_VIEW;

MEASUREMENT_VIEW;

OBSERVATION_VIEW;

PROCEDURE_VIEW;

COVID_LAB_VIEW;

ALL_SOURCE_CONCEPTS;

PATIENT_DIMENSION;

VISIT_DIMENSION;

DEVICE_VIEW;

Step 5: Build CONCEPT DIMENSION using

create_omop_act_concept_dimension script will load the concept dimension using the ACT OMOP metadata tables

Example for sql db instance, run create_omop_act_concept_dimension.sql

Note: The concept_Dimension is populated from metadata tables.

Verify create_omop_act_concept_dimension.sql to ensure it has complete metadata tables information before

running the script

Example: the ACT/OMOPVital_Signs information should be in the script to load the ACT/OMOPVital_Signs concept data

Step 6: 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

Note:

The Lab metadata tables should have data in the C_METADATAXML column in order for the lab values to be queryable from UI

If the C_METADATAXML is missing from the source ontology Lab metadata file, you can load the values from the standard i2b2-ACT Lab metadata table.