When setting up your Metadata (ONT) database, you will be creating a number of database tables and some SQL-based procedures.
When your metadata database is installed, it will have the following tables (per i2b2 v1.8.1):
- TABLE_ACCESS: a configuration table that tells i2b2 which ontology tables to load into the user interface (required)
- SCHEMES: a configuration table that tells i2b2 which coding schemes are being used in the ontology tables (required, but may be empty)
- one or more "ontology" tables (required):
- each ontology table will typically consist of a hierarchy of concepts for a particular category or domain of healthcare data; for instance:
- in the i2b2 demo ontology, the I2B2 table contains concepts for patient demographics
- in the ACT ontology, the ACT_DEM_V41 table contains concepts for patient demographics
- each ontology table will typically consist of a hierarchy of concepts for a particular category or domain of healthcare data; for instance:
- CUSTOM_META: an empty ontology table; may include custom concepts added by you
- totalnum and totalnum_report: tables dedicated to recording the number of patients who have the concepts present in the ontology trees; these tables are NOT displayed to the user as part of the ontology tree in the user interface; these table are empty until you run a "totalnum" report (see Ontologies 102 – Patient Counts ("
totalnum"))
After installation, all required tables will be populated, indexed, and ready to use.
After installation, there will also be a number of SQL-based procedures added to the ONT database, to prepare for running the "totalnum" report
The table below shows all the tables you should expect to find in your ONT database when you have loaded your i2b2 ontology (per i2b2 v1.8.1):
| i2b2 Demo Ontology | ACT Ontology | ACT-on-OMOP Ontology |
|---|---|---|
BIRN CUSTOM_META I2B2 ICD10_ICD9 ONT_PROCESS_STATUS PHI SCHEMES TABLE_ACCESS totalnum totalnum_report | ACT_COVID_V41 ACT_CPT4_PX_V41 ACT_DEM_V41 ACT_HCPCS_PX_V41 ACT_ICD10_ICD9_DX_V4 ACT_ICD10CM_DX_V41 ACT_ICD10PCS_PX_V41 ACT_ICD9CM_DX_V4 ACT_ICD9CM_PX_V4 ACT_LOINC_LAB_V4 ACT_LOINC_LAB_PROV_V41 ACT_MED_ALPHA_V41 ACT_MED_VA_V41 ACT_RESEARCH_V41 ACT_SDOH_V41 ACT_VAX_V41 ACT_VISIT_DETAILS_V41 ACT_VITAL_SIGNS_V4 ACT_ZIPCODE_V41 BIRN CUSTOM_META I2B2 ICD10_ICD9 ONT_PROCESS_STATUS SCHEMES TABLE_ACCESS totalnum totalnum_report | ACT_COVID_V41_OMOP ACT_CPT4_PX_V41_OMOP ACT_DEM_V41_OMOP ACT_HCPCS_PX_V41_OMOP ACT_ICD10_ICD9_DX_V4_OMOP ACT_ICD10CM_DX_V41_OMOP ACT_ICD10PCS_PX_V41_OMOP ACT_ICD9CM_DX_V4_OMOP ACT_ICD9CM_PX_V4_OMOP ACT_LOINC_LAB_V4_OMOP ACT_LOINC_LAB_PROV_V41_OMOP ACT_MED_ALPHA_V41_OMOP ACT_MED_VA_V41_OMOP ACT_RESEARCH_V41_OMOP ACT_SDOH_V41_OMOP ACT_VAX_V41_OMOP ACT_VISIT_DETAILS_V41_OMOP ACT_VITAL_SIGNS_V4_OMOP ACT_ZIPCODE_V41_OMOP BIRN CUSTOM_META I2B2 ICD10_ICD9 ONT_PROCESS_STATUS SCHEMES TABLE_ACCESS totalnum totalnum_report |
This diagram shows how tables from the Ontology cell enable content in the i2b2 webclient:
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