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For instance, if you recall (from your high-school biology class) Linnaeus's "binomial nomenclature" model of how to name living organisms, then you already know what a taxonomy is. For instance, the common house fly Musca domestica and other flies in the family Muscidae are members of the order Dipte ra, which are organisms in the class Insecta, phylum Arthropoda, kingdom Animalia. A taxonomy defines the hierarchical "is-a" relationship between two concepts. SimilarlyAs another example, a Camry is a Toyota, which is an automobile, which is a type of motorized, wheeled conveyance.
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The i2b2 database-loading modules come with at least 3 sets of "metadata" or ontology trees. These are the demo ontology, the ACT ontology, and the ACT-on-OMOP ontology.
| Name | Description | Target Data Model |
|---|---|---|
| i2b2 Demo Ontology | default metadata from i2b2 authors | i2b2 Common Data Model (star-schema); default CRC demo database has matching concepts |
| ACT Ontology | ENACT project | i2b2 Common Data Model (star-schema); ACT CRC demo database has matching concepts |
| ACT-on-OMOP Ontology | ENACT project | i2b2 Common Data Model (star-schema), but modified with views into the OMOP Common Data Model; the CRC database loaded with SYNPUF demo data has matching concepts |
The table below outlines the domains and coding schemes included in each ontology.
| Domain / Coding Scheme | i2b2 Demo Ontology | ACT Ontology | ACT-on-OMOP Ontology |
|---|---|---|---|
| Demographics | |||
Diagnoses | |||
| ICD-9-CM |  | | |
| ICD-10-CM | Out of date | | |
| SNOMED CT | | ||
Medications | Homegrown? | ||
RxNorm | | ||
NDC | | ||
SNOMED CT | | ||
| Procedures | |||
| ICD-9-CM | | | |
| ICD-10-PCS | | ||
| CPT-4 | | ||
| HCPCS | | ||
| SNOMED CT | | ||
| Lab Tests / Vital Signs | Homegrown? | ||
| LOINC | | ||
| SNOMED CT | |
| Info |
|---|
| If your local institution does not have data in the CRC database for a certain domain in your chosen i2b2 ontology, then user queries referencing that domain may come back empty. To avoid that, you can exclude that domain from the i2b2 user interface, so that the domain without matching data in the CRC database is never used in a query. |
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This table shows all the tables you should expect to find in your ONT database when you have loaded your i2b2 ontology:
| 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 |
In addition, in your CRC database, there should be a CONCEPT_DIMENSION table.
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