Course at EMBL-EBI

Ensembl REST API workshop

The Ensembl project provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. Our sister project Ensembl Genomes covers bacteria, plants, fungi, protists and (invertebrate) metazoa. This workshop is aimed at researchers and developers interested in exploring the data beyond the websites. The workshop covers how to use the Ensembl REST APIs, including understanding the major endpoints and how to write Python/R/Perl scripts to call them.

Who is this course for?

Bioinformaticians and wet-lab biologists who can program in Perl, Python or R. The Ensembl browser workshop is a pre-requisite for this course.

What will I learn?

Learning outcomes

After this course participants should be able to:

  • Synthesise the data types accessible through the Ensembl REST API
  • Understand the methods in the Ensembl REST API
  • Navigate the Ensembl REST API documentation to find available methods
  • Write Python/R/Perl scripts to access data via the Ensembl REST API


Astrid Gall


09:30-10:00    Overview of the Ensembl REST API
10:00-11:00    Accessing GET queries with the Ensembl REST API
11:00-11:20    Tea/Coffee Break    
11:20-12:30    Decoding json and chaining REST queries together
12:30-13.15    Lunch
13:15-14:30    Accessing POST queries with the Ensembl REST API
14:30-15:00    Rate limiting

Attendance at this workshop is allocated on a first come, first served basis.

This course does not cover the background to the Ensembl data and participants should have previously attended an Ensembl browser course (such as the one on the 15th October). This course does not cover the basics of programming.

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Ensembl training

16 October 2019
European Bioinformatics Institute United Kingdom
Astrid Gall

  • Astrid Gall

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