Utilizing i2b2's reusable application programming interface (API) to support OMOP data model. 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.
First, download the necessary components onto a computer that can connect to your target database and from which you can run SQL queries.
ant -f data_build.xml db_demodata_load_data
This will create act-omop Views and loads the concept_dimension table with act-omop concepts data
You will need to drop PATIENT_DIMENSION and VISIT_DIMENSION before you load any data. |
ant -f data_build.xml db_metadata_load_data
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
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 |
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; |