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Introduction

 

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.

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  • 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.

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Here is another screenshot, where you can see the expansion for "Race" in the "Demographics" tree:

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Where do i2b2 ontology "concepts" come from?

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Part 2: Choosing Your Ontology

 

Do all i2b2 instances share the same i2b2 ontology?

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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. 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, where m is the version number and n is the release identifier.

Each ontology is designed to be used with some version of the i2b2 Common Data Model.

Name

FolderDescriptionWhen To UseTarget Data Model
i2b2 Demo Ontologydemodefault metadata from i2b2 authors; legacy categoriesdemonstrationi2b2 Common Data Model (star-schema)
; default CRC demo database has matching concepts
ACT Ontology
ENACT project
actmodern categories and concepts, supplied by the ENACT projectproductioni2b2
i2b2
Common Data Model (star-schema)
; ACT CRC demo database has matching concepts
ACT-on-OMOP Ontologyact-omopmodern categories and concepts, supplied by the ENACT projectproduction, at sites using OMOP CDMmulti-fact-table-enhanced i2b2 Common Data Model (star-schema)
, but modified with views into the OMOP Common Data Model; the CRC database loaded with SYNPUF demo data has matching concepts

To view and compare details of the domains and coding schemes included in each ontology, see Appendix B.

Info
titlei2b2 Common Data Model

A Common Data Model (CDM) is a way of organizing data into standardized structures and observational content to enable alignment of patient data across multiple organizations. Each i2b2 ontology leverages the i2b2 Common Data Model (CDM), which is based on a "star schema": instead of separate tables for diagnoses, medications, and other data types, all patient observations are stored in a single "fact" table, and the ontology describes the different codes that are placed in this fact table.

How should I choose which ontology to use?

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Part 3: How Ontologies and Patient Data Are Tied Together

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How does it work? How does the i2b2 ontology make the patient data queryable?

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Ontology Working Group OWL