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
Both the ACT-OMOP Ontology tables, views and data is available under edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata\act-omop folder.
Navigate to the Metadata folder and execute below steps:
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. |
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
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 |