Ensembl provides a popular genome browser for exploring genes and other genomic features.

While the Ensembl genome browser on the web is ideal for single genes, accessing data across groups of genes or features is more efficient via programmatic or file based means. Ensembl provides database access via Ensembl Perl API or MySQL, and access to files in a file transfer protocol (FTP) site divided into taxa for vertebrates, plants, fungi, bacteria and other Ensembl Genomes species. These services will remain available for use after summer 2026 but will not receive updates.

The new Ensembl has programmatic access provided via Ensembl GraphQL and refget. Data files for the new Ensembl are accessible from a new FTP site serving all species together in the same location. 

This webinar will present information on accessing genome data at large scales with some examples tailored for the new Ensembl platform.

This event is part of the 3-part webinar series Ensembl transition webinars: New genomes, access methods, and educational resources from Ensembl. You can follow the link for more information about the series and its webinars.

Who is this course for?

This webinar is suitable for programmatic users, users of Ensembl’s APIs, MySQL, or FTP services, bioinformaticians and computational biologists.

Outcomes

By the end of this webinar, participants will be able to:

• Describe the key differences of programmatic access services between Ensembl versions
• Identify the file formats available via the Ensembl FTP sites 
• Browse the new Ensembl GraphQL and refget documentation for accessing the latest genome data

This webinar, hosted on Zoom Webinar, is free to attend, but you need to register for a place beforehand, using the 'Register' button. Once registered, you will receive a confirmation email with a link to join the webinar.

The webinar will be recorded, and the recording will be made available on this page one day after the event. Please note that we do not issue certificates of attendance for our webinars. However, you will receive an email from our Zoom account confirming your participation a day after the event