Developers Getting Started With i2b2
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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 to support OMOP data model. Below steps involve creating datamodel-specific i2b2 ontologies and mapping these to query non-standard OMOP table structureThe 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.

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Steps to build ACT-OMOP Ontology

Step1: Create OMOP tables and load data using:

 OMOP


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 (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.
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)
        • This step can be skipped if you already have OMOP on your target 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:
      • 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  In 3.4.5 for now.    , are we going to include a concept_dimension or the build script to run at the end?  


    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


    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: 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


    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


    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.

    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

    These are the ACT-OMOP views:

    CONDITION_VIEW;

     DRUG_VIEW;

     MEASUREMENT_VIEW;

     OBSERVATION_VIEW;

    PROCEDURE_VIEW;

    COVID_LAB_VIEW;

     ALL_SOURCE_CONCEPTS;

     PATIENT_DIMENSION;

     VISIT_DIMENSION;

     DEVICE_VIEW;