The Ensembl genome browser and REST API to retrieve genome annotation data

The Ensembl project provides freely available access to genome annotation datasets including gene, variant and regulatory feature annotation as well as comparative genomics analyses for over 300 vertebrate species and 30,000 non-vertebrate eukaryotes and prokaryotes. All of the data can be retrieved through Ensembl’s online genome browsers (www.ensembl.org, www.ensemblgenomes.org and rapid.ensembl.org) as well as programmatically via Ensembl’s REST API.

This workshop will introduce you to the range of data available through Ensembl and the appropriate platforms to visualise and extract it for analysis and interpretation. The morning sessions of this workshop will guide you through the Ensembl genome browser and BioMart interfaces to show you how to explore and retrieve both small and large-scale datasets. In the afternoon session, this workshop will introduce you to the concepts of the Ensembl REST API and guide you through the principles of retrieving Ensembl data programmatically using both Python and R.

To participate in the hands-on aspects of this workshop, including live polling, exploring online databases and exercises, you will need to bring a laptop. Workshop materials, including slides, screenshots, exercises, sample files and solutions will be available before the workshop and will remain permanently online at the Ensembl training portal: https://training.ensembl.org.

The event page, which will have the full set of materials closer to the date: https://training.ensembl.org/events/2023/2023-11-02-ISCB_Academy

Time/Date:

• Part 1: Nov 2, 2023 at 3:00 PM UTC
• Part 2: Nov 3, 2023 at 3:00 PM UTC

Learning objectives

• Outline the different data types available through Ensembl
• Identify the appropriate methods for data retrieval from Ensembl
• Visualise and retrieve genome annotation data through the online Ensembl genome browser
• Export custom datasets from Ensembl using the BioMart export tool
• Perform queries and extract data returned from the Ensembl REST API

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License

This work is licensed under a Creative Commons Attribution 4.0 International License.