Developers Getting Started With i2b2
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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.

Steps to build ACT-OMOP Ontology

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.

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

  • OMOP: 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.
    • This step can be skipped if you already have OMOP on your target database.
  • If you have not installed i2b2 previously (i.e. you are not setting this up as an i2b2 Project in a larger installation):
  • 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 3.4.5. Run the ant command:

                                    ant -f data_build.xml db_demodata_load_data

This will create act-omop Views and loads the concept_dimension table with act-omop concepts data

You will need to drop/rename PATIENT_DIMENSION and VISIT_DIMENSION tables before you load any data.

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, 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\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

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.

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

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


Both the ACT-OMOP Ontology tables, views and data is available under\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:











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