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A tutorial on using Open Biological and Biomedical Ontologies (OBO) to create better biodata
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OBO Tutorial (for OHSU BioData Club)

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 the tutorial's developer, James Overton, 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. This version of the tutorial has been modified by Marijane White of the OHSU Library for use in the Better BioData ontology workshop hosted by OHSU's BioData Club.

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.

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


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.


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


Copyright © 2019, James A. Overton and OHSU Library

Distributed under the CC-by 3.0 License:

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