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i2b2-on-OMOP With ENACT-OMOP Ontology v4.1

i2b2-on-OMOP With ENACT-OMOP Ontology v4.1

Apr 04, 2024

 

Design

Utilizing i2b2's reusable application programming interface (API), the OMOP data model is now supported. The ENACT-OMOP ontology queries OMOP table views that correspond to the OMOP table structure. The i2b2 query tool tables and ENACT-OMOP ontology are installed in a he 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.

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: Install i2b2, with ACT-OMOP core tables, views, and ontologies.

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

 

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.

 

The CPT4 ontology table is not included with i2b2 due to AMA restrictions on redistribution of CPT code information. Contact the ACT team to get a copy if your institution is an AMA member.

Step 3: Advanced Users - Create Project

If an OMOP project will coexist with an i2b2 project, set up an i2b2 OMOP project pointing to the i2b2-OMOP database that you just configured.  

6.6.0. 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_<version no>\NewInstall\Metadata\act-omop folder.

The scripts are in this folder:

 

 

 

 

 

 

 

 

 

 

 

 

These are the ACT-OMOP ontology tables.

ACT_ICD10CM_DX_V41_OMOP

ACT_ICD10PCS_PX_V41_OMOP

ACT_ICD9CM_DX_V41_OMOP

ACT_ICD9CM_PX_V41_OMOP

ACT_HCPCS_PX_V41_OMOP

ACT_MED_ALPHA_V41_OMOP

ACT_MED_VA_V41_OMOP

ACT_LOINC_LAB_PROV_V41_OMOP

ACT_LOINC_LAB_V41_OMOP

ACT_SDOH_V41_OMOP

ACT_VITAL_SIGNS_V41_OMOP

ACT_VISIT_DETAILS_V41_OMOP

ACT_COVID_V41_OMOP

ACT_DEM_V41_OMOP

ACT_ICD10_ICD9_DX_V41_OMOP

ACT_RESEARCH_V41_OMOP

ACT_VAX_V41_OMOP

ACT_ZIPCODE_V41_OMOP

These are the ACT-OMOP views:

EMPTY_VIEW; * this is actually an empty table

CONDITION_VIEW;

DRUG_VIEW;

MEASUREMENT_VIEW;

OBSERVATION_VIEW;

PROCEDURE_VIEW;

COVID_LAB_VIEW;

PATIENT_DIMENSION;

VISIT_DIMENSION;

DEVICE_VIEW;

CONDITION_NS_VIEW;

DRUG_NS_VIEW;

MEASUREMENT_NS_VIEW;

OBSERVATION_NS_VIEW;

PROCEDURE_NS_VIEW;

DEVICE_NS_VIEW;

VISIT_NS_VIEW;