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Ensembl REST API workshop



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 using the REST API to query the core, variation, compara and functional genomics (regulation) databases. 



Denise Carvalho-Silva, EMBL-EBI


Audience and Prerequisites

  • Bioinformaticians and wet-lab biologists who can program
  • Some basic programming experience is a prerequisite for the course. The REST API works for any language, but in the workshop we can only offer assistance to PERL and Python programmers
  • Beginner and regular users of the Ensembl API are welcome
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals


Syllabus, Tools and Resources

During this course you will learn about:

  • Introduction to Ensembl: Data models, features
  • APIs in Ensembl: Perl and REST, navigate documentation
  • Overview of REST and Functional groupings.
  • Accessing genomic regions (slices), genes, transcripts, translations and repeats.
  • Accessing genomic variants, their alleles and allele frequencies, genotypes, phenotypes, linkage disequilibrium and genes they hit.
  • Accessing gene trees, homologues and families.
  • Accessing Regulatory Features, identifying variants within features.


Learning Objective

After this course you should be able to:

  • Understand the data types accessible through the Ensembl REST API
  • Understand the methods in the Ensembl REST API
  • Practice using the Ensembl REST API to access data



Book Here

Ensembl training materials

Ensembl Perl API Documentation

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