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Utilizing i2b2's reusable application programming interface (API), the OMOP =
data model is now supported. The ENACT-OMOP ontology queries OMOP table vie=
ws 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 applic=
ation layer are loaded. With the ontology, it becomes possible to query OMO=
P tables using the i2b2 interface. The design document can be found <=
a href=3D"https://docs.google.com/document/d/1M6aT4ff5EJ34xobf6iWzQCQO39kOz=
jNUKAS2WDSNY40/edit?usp=3Dsharing" class=3D"external-link" rel=3D"nofollow"=
>here.
First, download the necessary components onto a computer that can connec= t to your target database and from which you can run SQL queries.
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_proc=
edures_release_1-7
ant -f data_build.xml db_demodata_load_data
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
Be sure to drop/rename PATIENT_DIME= NSION and VISIT_DIMENSION tables before you run the db_demodata_load_data a= nt target.
The Lab metadata tables should have data in = the C_METADATAXML column in order for the lab values to be queriable from U= I
If the C_METADATAXML is missing from t= he source ontology Lab metadata file, you can load the values from the stan= dard i2b2-ACT Lab metadata table.
The CPT4 ontology table is not includ= ed with i2b2 due to AMA restrictions on redistribution of CPT code informat= ion. 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 th= at you just configured.
6.6.0. Guide to creatin= g a new project with the admin tool.
Verify the Ontology is displayed and queriab= le from the webclient
Notes
Both the ACT-OMOP Ontology tables, vie= ws and data is available under edu.harvard.i2b2.data\Release_1-7\NewIn= stall\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 A= CT_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_S= DOH_V41_OMOP ACT_VITAL_SIGNS_V41_OMOP ACT_VISIT_DETAILS_V41_OMO= P ACT_COVID_V41_OMOP ACT_DEM_V41_OMOP ACT_ICD10_ICD9_DX_V= 41_OMOP ACT_RESEARCH_V41_OMOP ACT_VAX_V41_OMOP ACT_ZIPCOD= E_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; PA= TIENT_DIMENSION; VISIT_DIMENSION; DEVICE_VIEW; CON= DITION_NS_VIEW; DRUG_NS_VIEW; MEASUREMENT_NS_VIEW; OBSERV= ATION_NS_VIEW; PROCEDURE_NS_VIEW; DEVICE_NS_VIEW; VISIT_NS_VIEW; |