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OBO Tutorial

The Open Biological and Biomedical Ontologies (OBO) provide a suite of high-quality, interoperable, free and open source tools for sharing scientific knowledge and making new discoveries.

This tutorial reflects the lessons that I've learned using OBO ontologies to work with scientific data. You'll learn how to use OBO ontologies to communicate more clearly, to integrate data, and to improve search and analysis.

We use a single running example to keep things concrete: a spreadsheet of data about histology observations. Starting with this data, we build an application ontology, transform the data into linked data, and then apply an automated reasoner and query over it. All using open source code and tools.

Get Started!

  1. Introduction
  2. Names and Naming
  3. Open Biological and Biomedical Ontologies (OBO)
  4. Using and Reusing Ontologies
  5. Processing Data with Ontologies
  6. Updating, Testing, and Releasing Ontologies

Download PDF and code

NOTE: This is still a work in progress. Not all of the sections are complete.

Other Resources

Here are some links to other resources for learning about OBO:


To read through the tutorial and look at most of the files, all you need is a web browser. To view the OWL files you should use the desktop version of Protégé.

If you want to dig deeper, see code/


Here's a quick overview of the repository:

  • docs: the tutorial content in Markdown format
  • examples: data and code files referred to in the tutorial
  • images: supporting images
  • code: more elaborate code examples to support the tutorial
  • bin: other code for working with the tutorial


Corrections, improvements, suggestions, bug reports, etc. are all very much appreciated! Please:


Copyright © 2017, James A. Overton

Distributed under the CC-by 3.0 License:


A tutorial on using Open Biological and Biomedical Ontologies (OBO)


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