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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

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• ; it will be found in both the "Diagnoses" tree and in the "Diagnoses (ICD10)" tree;
• aspirin is a non-steroidal anti-inflammatory drug, which is a type of medication; it will be found in the "Medications" tree;
• tonsillectomy is a type of surgery, which is a procedure; it will be found in the "Procedures" tree;
• hemoglobin A1c is a blood test, which is a type of

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• laboratory test; it will be found in the "Laboratory Tests" tree; and
• gender or sex is a patient-demographic descriptor; it will be found in the "Demographics" tree.

How does it work?

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How does

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the i2b2 ontology make the patient data queryable?

A)

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The ontology is 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.

B) The i2b2 ontology in the i2b2 metadata database works together with the patient data in the i2b2 CRC database. Each patient "observation" in the CRC database must have a code associated with it, and that code must match a healthcare concept — diagnosis, procedure, medication, lab test, demographic descriptor, etc. — that exists in the metadata database. For instance, if the patient's electronic health record indicates that the patient had the procedure "tonsillectomy with adenoidectomy," then that fact needs to be recorded in the CRC database  using the standard code for that particular procedure. In the case of using the default i2b2 Procedures metadata tree, that code would be "ICD9:28.3". So the CRC patient data will be queryable in i2b2 only if the patient facts in the CRC database are recorded utilizing standard codes that are referenced in the i2b2 metadata (ontology trees).

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

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No. Several i2b2 ontologies have been developed and are openly available for use. Any organization may also modify an existing ontology for it's its own use, or develop a new ontology. (See Ontologies 201.)

What ontologies can I use right away ('out of the box')?

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