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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




Steps to build ACT-OMOP Ontology


Step1: Create OMOP tables and load data using:


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
      • 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 3.4.5 for now.    


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\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


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

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

CONDITION_VIEW;

 DRUG_VIEW;

 MEASUREMENT_VIEW;

 OBSERVATION_VIEW;

PROCEDURE_VIEW;

COVID_LAB_VIEW;

 ALL_SOURCE_CONCEPTS;

 PATIENT_DIMENSION;

 VISIT_DIMENSION;

 DEVICE_VIEW;



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

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


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



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