Online tutorial

Ensembl REST API

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Time to complete:

1 hour

This course includes:

  • Activities
  • Videos

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Last reviewed:

February 2021


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All materials are free cultural works licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, except where further licensing details are provided.


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The Ensembl REST API provides language-agnostic programmatic access to genomic data in the Ensembl database. This course uses Jupyter Notebooks hosted by Google Colab to walk you through the APIs and practise writing scripts to access these data. A video provides a brief overview of the REST API, endpoints and instructions on working with the Jupyter notebooks.

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Who is this course for?

This is an intermediate to advanced level course and requires some familiarity with Ensembl, REST APIs and the ability to program in Python or R. We won’t teach you how to code in this course, just how to use your existing coding knowledge to access Ensembl data. If you would like an introduction to Ensembl then we recommend watching our Ensembl Browser Webinar Series.

What will I achieve?

By the end of the course you will be able to:

  • Describe the data types accessible through the Ensembl REST API
  • Describe the methods in the Ensembl REST API
  • Navigate the Ensembl REST API documentation to find available methods
  • Write scripts to access data via the Ensembl REST API

What resources do I need?

To copy the Jupyter notebooks you will need to sign in with a (free) Google account, or you can download them if you have Jupyter installed. Please view the page 'Familiarise yourself with Jupyter Notebooks' for more details. 

DOI: 10.6019/TOL.Ensembl_API-t.2018.00001.1

Course contents