THIS FEATURE WILL BE AVAILABLE MARCH 2023

Objective

Utilize the concept of a reusable

Design

Utilizing i2b2's reusable application programming interface (API)

by using i2b2 API to adapt and support

, the OMOP data model

. Below steps involve creating datamodel-specific i2b2 ontologies and mapping these to query non-standard OMOP table structure

Steps to Create and Load ACT-OMOP Ontology

Step1: Create OMOP tables and load data using:

OMOP

is now supported. The ENACT-OMOP ontology queries OMOP table views that correspond to the OMOP table structure. The i2b2 query tool tables and ENACT-OMOP ontology are installed in a he 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.

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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 newi nstall 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: Install i2b2, with ACT-OMOP core tables, views, and ontologies.

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.

It

- - This 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

For 3.4.5

i2b2: You will be installing i2b2 as explained in the installation guide. Follow the chapters in the installation guide, but see the notes in the next bullet on Chapter 3.
Chapter 3. Data Installation requires special handling. All the steps in the installation guide should be followed except for the following changes in the CRC and Metadata sections::
- You need to select the act-omop project for Metadata and CRC. Specifically, in 3.4.2 Set Database Properties (CRC) and 3.7.2 Set Database Properties (Metadata), 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.

- to set db.project parameter to act-omop.

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

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

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Navigate to the Metadata folder and execute below steps:

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

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- Instead of CRC install step 3.4.4, drop the patient_dimension and visit_dimension tables from the database. For convenient reference, the correct steps 3.4.3-3.4.5 are summarized here:
  ant -f data_build.xml create_crcdata_tables_release_<version no>
  FROM THE DATABASE: DROP PATIENT_DIMENSION; DROP VISIT_DIMENSION;
  ant -f data_build.xml create_procedures_release_<version no>
  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. The first two steps create the standard CRC tables and procedures.
- 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.

- data

1-7

. This will

Create and load
- Make sure i2b2 is configured for multiple fact tables by changing the appropriate entry in the database.
  - 3.11 Multiple Fact Tables

Info
Be sure to drop/rename PATIENT_DIMENSION and VISIT_DIMENSION tables before you run the db_demodata_load_data ant target.

Info

The Lab metadata tables should have data in the C_METADATAXML column in order for the lab values to be queriable 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.

Info
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 3: Advanced Users - Create Project

If an OMOP project will coexist with an i2b2 project, set up an i2b2 OMOP project pointing to the i2b2-OMOP database that you just configured.

6.6.0. 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_<version no>\NewInstall\Metadata\act-omop folder.

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The scripts are in this folder:

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These are the ACT-OMOP ontology tables.

ACT_ICD10CM_DX_

V4

V41_OMOP

ACT_ICD10PCS_PX_

V4

V41_OMOP

ACT_ICD9CM_DX_

V4

V41_OMOP

ACT_ICD9CM_PX_

V4

V41_OMOP

ACT_

CPT4_PX_V4_OMOPACT_

HCPCS_PX_

V4

V41_OMOP

ACT_MED_ALPHA_

V4

V41_OMOP

ACT_MED_VA_

V4

V41_OMOP

ACT_

MED

LOINC_

VA

LAB_

V4

PROV_V41_OMOP

ACT_LOINC_LAB_

PROV

V41_

V4_

OMOP

ACT_SDOH_

V4

V41_OMOP

ACT_VITAL_SIGNS_

V4

V41_OMOP

ACT

ACT_VISIT_DETAILS_

V4

V41_OMOP

ACT_COVID_

V4

V41_OMOP

ACT_DEM_

V4

V41_OMOP

ACT_ICD10_ICD9_DX_

V4

V41_OMOP

Create the ACT-OMOP views by executing BUILD_ACT_OMOP_VIEWS_ALL_MSSQL.sql

ACT_RESEARCH_V41_OMOP

ACT_VAX_V41_OMOP

ACT_ZIPCODE_V41_OMOP

These are the ACT-OMOP views:

EMPTY_VIEW; * this is actually an empty table

CONDITION_VIEW;

DRUG

DRUG_VIEW;

MEASUREMENT

MEASUREMENT_VIEW;

OBSERVATION

OBSERVATION_VIEW;

PROCEDURE_VIEW;

COVID_LAB_VIEW;

ALL

PATIENT_

SOURCE_CONCEPTS

DIMENSION;

PATIENT

VISIT_DIMENSION;

VISIT

DEVICE_

DIMENSION

VIEW;

DEVICE

CONDITION_NS_VIEW;

Step 4: Build ACT-OMOP CONCEPT DIMENSION

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

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Info

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 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

Info

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.

DRUG_NS_VIEW;

MEASUREMENT_NS_VIEW;

OBSERVATION_NS_VIEW;

PROCEDURE_NS_VIEW;

DEVICE_NS_VIEW;

VISIT_NS_VIEW;

ETL OMOP data

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

Versions Compared

Old Version 7

New Version Current

Key

THIS FEATURE WILL BE AVAILABLE MARCH 2023

Objective

Design

Steps to Create and Load ACT-OMOP Ontology

Step 1: Acquire downloads

Step 2: Install i2b2, with ACT-OMOP core tables, views, and ontologies.

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

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

Image Removed

Image Added

Step 4: Build ACT-OMOP CONCEPT DIMENSION

Step 5: Create Project

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Page History

Versions Compared

Old Version 7

New Version Current

Key

THIS FEATURE WILL BE AVAILABLE MARCH 2023

Objective

Design

Steps to Create and Load ACT-OMOP Ontology

Step 1: Acquire downloads

Step 2: Install i2b2, with ACT-OMOP core tables, views, and ontologies.

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

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

Image Removed

Image Added

Step 4: Build ACT-OMOP CONCEPT DIMENSION

Step 5: Create Project

Pages

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