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What is an ontology?

"Ontology" — as an abstract noun — represents branches represents the branch of Philosophy that discuss discusses "existence." But in Information Science, an "ontology" — as a concrete noun — is a way of showing listing the properties attributes of a subject area and showing how they are related, by defining . An ontology for a subject area or "domain" consists of a set of terms and relational expressions that represent the entities in that subject areathat domain, along with a set of expressions that define how the entities are related to each other.

In i2b2's domain of Clinical Research Informatics, an ontology is a collection of healthcare-related "concepts," that define a set of terms representing " or terms. These terms represent the various categories of information in clinical and translational science. Categories such as demographics, diagnoses, procedures, laboratory tests, and medications are described using hierarchical lists of "concepts" in an i2b2 ontology.

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First, a little more terminology. The i2b2 "patient data" are stored in the Clinical Research Chart database, or "CRC database." The concepts that describe those patient data are known as the "metadata." The metadata or ontology is are stored in the Metadata database, or "ONT database."

The i2b2 metadata in the ONT database work together with the patient data in the 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. 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 treesONT 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". A When a researcher makes a query in the user interface for "tonsillectomy with adenoidectomy," that query will be translated by i2b2 into a query in the CRC database for patients who have the code ICD9:28.3 in their CRC data records.

A) 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.

Where did the i2b2 ontology "concepts" come from?

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