[BC]2 Basel Computational Biology Conference tutorial: Using the Ensembl REST APIs to programmatically access genomic data, 9 September 2019


  Monday 9 September 2019


University of Basel - Petersplatz 1, P. O. Box, 4001,  Basel, Switzerland

Application opens: 

Tuesday 16 July 2019

Application deadline: 

Friday 06 September 2019


First come, first served


Astrid Gall

Registration fee: 

120 CHF

Course Overview

The Ensembl project provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. This workshop is aimed at researchers and developers interested in exploring Ensembl beyond the website. The workshop covers how to use the Ensembl REST APIs, including understanding the major endpoints and how to write Python/Perl/R scripts to call them.

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.

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


Time Details
09:00-10:00 Introduction to Ensembl and its data types
10:00-10:30 Overview of the Ensembl REST API
10:30-11:00 Accessing GET queries with the Ensembl REST API
11:00-11:20 Tea/Coffee Break
11:20-13:30 Decoding json and chaining REST queries together
13:30-14:30 Lunch
14:30-15:30 Accessing POST queries with the Ensembl REST API
15:30-16:00 Rate-limiting