Developers Getting Started With i2b2
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PREVIEW VERSION AVAILABLE NOW. FINAL VERSION WILL BE

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RELEASED IN DECEMBER 2023.

Objective

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Design

Utilizing i2b2's reusable application programming interface (API) 

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to support OMOP data model.

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 to query non-standard OMOP table structure

Step1: Create OMOP tables and load  data using

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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.

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      • This can cause problems during ETL.

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

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  • 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.

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      • In 3.4.

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      • 2, edit the CRC db properties file

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      • 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

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ontology data load process

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  • 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 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_

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data  

      • This will execute the  SQL scripts from the edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata\act-omop\scripts\<db type> folder and

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      • :
        • Creates ACT-OMOP v4 Ontology metadata tables with indexes. 

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        • 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

Step 4: Create OMOP views. 

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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;

 Step 5: 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 

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 6: 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

Note: 

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.