Developers Getting Started With i2b2
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THIS FEATURE

PREVIEW VERSION AVAILABLE NOW. FINAL VERSION WILL BE

AVAILABLE MARCH

RELEASED IN DECEMBER 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 to support 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

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.

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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.

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.
    • It
      • This can cause problems during ETL.
  • ETL OMOP data

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)
  • If you have not installed i2b2 previously (i.e. you are not setting this up as an i2b2 Project in a larger installation):
  • Make sure i2b2 is configured for multiple fact tables by changing the appropriate entry in the database.
  • 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:
    • For
        • In 3.4.
    5
        • 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.
        • to set db.project parameter  to act-omop.             
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        • Perform step 3.4.3-3.4.5 and drop/rename the PATIENT and VISIT_DIMENSION tables. E.g., run the commands:

                                 

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     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.

    Info

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


    Step 3: ACT-OMOP v4 ontology data load

    and Views creation

    process

    Both the
    • Follow the instructions in Chapter 3 of the i2b2 installation guide to create and load 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
    • 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. 

    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
        • and:
        Create and load
              • Creates ACT-OMOP v4 Ontology metadata tables with indexes. 
              • Loads the act-omop metadata


        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.


        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.

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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_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_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

        Create

        These are the ACT-OMOP views

        by executing BUILD_ACT_OMOP_VIEWS_ALL_MSSQL.sql

        :

        CONDITION_VIEW;

         DRUG_VIEW;

         MEASUREMENT_VIEW;

         OBSERVATION_VIEW;

        PROCEDURE_VIEW;

        COVID_LAB_VIEW;

         ALL_SOURCE_CONCEPTS;

         PATIENT_DIMENSION;

         VISIT_DIMENSION;

         DEVICE_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.