What is an ontology?
The idea of "Ontology" is an idea borrowed from philosophy, and it is used to discuss "existence."
In the realm of i2b2, an ontology is actually a "taxonomy," which is a hierarchical group of terms or concepts. 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, which are organisms in the class Insecta, phylum Arthropoda, kingdom Animalia. A taxonomy defines the hierarchical "is-a" relationship between two concepts. Likewise, a Camry is a Toyota, which is an automobile, which is a type of motorized, wheeled conveyance.
Why does i2b2 have an ontology?
An i2b2 instance requires an ontology so that researchers can locate "concepts" of interest. And one very helpful way for them to locate these concepts is by using a hierarchical tree, or taxonomy. When you log in to the demo i2b2 site (username "demo", password "demouser" are already filled in), you will see the i2b2 ontology tree on the upper left side of the user interface. We also refer to that listing as a group of ontologies, where each domain or top-level taxonomy is called an ontology in its own right.
In this screenshot, we would say that i2b2 is displaying an ontology tree with 13 top-level ontologies or domains, namely: Clinical Trials, Custom Metadata, Demographics, etc.
For instance, diabetes mellitus is an endocrine disorder, which is a type of diagnosis. Aspirin is a non-steroidal anti-inflammatory drug, which is a type of drug.
That may be the "demo" ontology, but it doesn't resemble the "ACT" ontology that our PI was showing us. How many different ontology trees does i2b2 have?
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.
How about a thumbnail description of these ontologies? How do they differ from each other?
Sure. Here is a table describing the major differences among them.
| Name | Description | Included Domains | 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 project | fixme | i2b2 Common Data Model (star-schema); ACT CRC demo database has matching concepts |
| ACT-on-OMOP ontology | ENACT project | fixme | 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 |
