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This tutorial page is intended for i2b2 administrators who are new to i2b2 and clinical informatics. Maybe you've been asked to deploy i2b2 for your institution. Maybe your institution already has an i2b2 instance, and you've just inherited it. You are curious about how things work and how to set up or modify the ontology database.

This page will bring you some insight.

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help you achieve these goals:

• Understanding what an ontology is for i2b2

• Choosing an appropriate ontology tree for i2b2

• Deploying an ontology tree for i2b2

• Understanding how the ontology enables queries in i2b2

Part 1: Ontology Basics

What is an ontology?

"Ontology" represents the branch of Philosophy that discusses "existence." But in Information Science, an "ontology" is a way of listing the attributes of a subject area and showing how these attributes are interrelated. An ontology for a subject area or "domain" consists of a set of terms that represent the entities in (or attributes of) that domain, along with a set of expressions that define how the entities in that domain are related to each other.

In i2b2's domain of "Clinical Research Informatics," an ontology is a collection of healthcare-related "concepts" or terms. These terms represent the various categories of information in clinical and translational science. Categories In an i2b2 ontology, categories such as Patient Demographics, Diagnoses, Procedures, Laboratory Tests, and Medications are described using hierarchical lists of "concepts." in an i2b2 ontology.

Unlike some other ontologies in Information Science, an i2b2 ontology does not typically define relationship expressions among the concepts or entities. Therefore, strictly speaking, an i2b2 ontology is generally more akin to a "taxonomy," which is a hierarchical group of terms or concepts, without any expressions defining the relationships among them.

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These concepts are rendered as a collection of nested folders and generally represent child-parent relationships. Researchers locate these concepts by using "drilling down" through a hierarchical tree, or by using the "search" tool. When you use the demo i2b2 site, you will see the i2b2 ontology tree on the upper-left side of the user interface. 

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Typically, the concepts that make up the various categories or "domains" are are based on medical terminology standards published by various institutions. Concepts can also be created ad hoc for a specific i2b2 instance by the i2b2 administrator at for that site. (For more information on custom metadata, please see Ontologies 201.)

The commonly used standards representing basic structured clinical patient data are represented by a number of different "coding schemes" — ICD-9, ICD-10, CPT-4, HCPCS, SNOMED CT, LOINC, RxNorm, UMLS, and VA Classes. We mention this here because these codes appear inside the ontology tables, and they are also referenced in the user interface. See Appendix B for further information.

There are many terms related to i2b2 ontologies that are new to me. Is there a Glossary?

Yes! Here is a Glossary that provides explainers for many of the key terms related to i2b2 ontologies and the i2b2 architecture.

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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 its own use, or develop a new ontology. (See Ontologies 201 – Custom Metadata – Additions and Modifications.)

The i2b2 software includes i2b2 ontologies that you can use right away. There are additional ontology trees that can substitute for, or can be added to, the standard i2b2 ontology trees. (See Appendix E – Advanced Ontologies.)

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The i2b2 database-loading modules come with at least 3 sets of "metadata" or ontology trees. These are the demo ontologyDemo Ontology, the ACT ontologyOntology, and the ACT-on-OMOP Ontology. Inside the i2b2 software release folder you will find the three ontology . tree folders (demo, act, and act-omop) at this location (linux syntax): i2b2/edu.harvard.i2b2.data/Release_m-n/NewInstall/Metadata

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