Ensembl REST API workshop, EBI, 16 October 2019


  Wednesday 16 October 2019


European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Monday 08 July 2019

Application deadline: 

Friday 11 October 2019


First come, first served


Astrid Gall

Registration fee: 


Registration closed

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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.

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.

Feedback from previous courses:

"Wish I had taken the course long time ago. Didn't know before how good and powerful APIs are!" API workshop, EMBL-EBI, January 2016

"I really enjoyed the course, and the ENSEMBL API will become a very relevant part of my toolset." API workshop, Cambridge, December 2013

If you think you'd like to host a similar course at your institute, you can find out more on the Ensembl workshops page.


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


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


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