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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 Diptera Dipte ra, which are organisms in the class Insecta, phylum Arthropoda, kingdom Animalia. A taxonomy defines the hierarchical "is-a" relationship between two concepts. Similarly, 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 Included Domains (I don't think all domains can be listed, or it will be hard to understand. I think this merges with description and tries to convey the level of detail and comprehensiveness). | Target Data Model | |
|---|---|---|---|
| i2b2 demo ontology | default metadata from i2b2 authors | fixme | i2b2 Common Data Model (star-schema); default CRC database has matching concepts |
| ACT ontology | ENACT projectfixme | i2b2 Common Data Model (star-schema); ACT CRC demo database has matching concepts | |
| ACT-on-OMOP ontology | ENACT projectfixme | i2b2 Common Data Model (star-schema), but modified with views into the OMOP Common Data Model; CRC database loaded with SYNPUF demo data has matching concepts |
The below table outlines the domains and standards included in each ontology. NOTE: if your local institution does not have data for a given domain that is included, such domains can easily be hidden or excluded.
| Domain/Standard | i2b2 Demo Ontology | ACT Ontology | ACT-on-OMOP Ontology |
|---|---|---|---|
| Demographics | |||
Diagnoses | |||
| --ICD-9CM |  | | |
| --ICD-10CM | Out of date | | |
Medications | Homegrown? | Rx-Norm | Rx-Norm |
| Procedures | |||
| --ICD-9 | | | |
| --ICD-10 | | | |
| --CPT-4 | | | |
| --HCPCS | | | |
| Lab Tests | Homegrown? | LOINC | LOINC |
How should I choose which ontology to use?
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