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An i2b2 instance requires an ontology so that researchers can locate "concepts" of interest and query data.

The medical concepts contained in an ontology are essentially the building blocks of an i2b2 query:
This is what “drives” the upper-left corner of the i2b2 webclient. In order to make facts or observations you wish to load into your i2b2 query-able, you must have corresponding entries in your ontology (that account for the codes used to represent these facts or observations).

These concepts are rendered as a collection of nested folders and are assumed to represent child-parent (or is-a) relationships. Researchers may locate these concepts . 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. 

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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.

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How does it work? (How does an ontology make the data queryable)

The ontology in made up of medical concepts. The ontology is visible to researchers through the webclient, and each medical concept in the ontology includes specific code(s) that match medical observation facts (such as diagnoses, medications, procedures, etc). A researcher can select concepts they are interested in to build a query, and medical data that matches those concepts' codes will be counted.

What are the sources of the concepts and domains? (Where do they come from?)

Typically, the concepts that make up domains are based on medical terminology standards. Some commonly used standards to represent basic structured clinical patient data collected in EHRs include:

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