Virtual course
Open Virtual Ensembl REST API Workshop
Work with Ensembl to master the Ensembl REST API and flexibly access genome-wide data, such as genes, variants, regulatory features, homologues and alignments.
Who is this course for?
Bioinformaticians and wet-lab biologists who can program in Python or R.
What will I learn?
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 scripts to access data via the Ensembl REST API
Course content
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.
During this course you will learn about:
- Introduction to Ensembl: Data models, features
- The Ensembl REST API, navigate documentation
- Overview of REST and functional groupings
- Accessing genomic regions (slices), genes, transcripts and translations
- Accessing genomic variants, their alleles and allele frequencies, genotypes and phenotypes
- Accessing gene trees and homologues
- Accessing regulatory features
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.
Trainers
Programme
Tuesday, 17th October 2023
19:00 - 17:00 (BST)
Overview of the REST API and how to query the REST API with URLs
Fetching REST endpoints programmatically
Wednesday, 18th October 2023
19:00 - 12:00 (BST)
Fetching specific data points from REST queries
Linking REST queries together
Thursday, 20th October 2023
19:00 - 12:00 (BST)
Bulk REST API queries with POST
Other data types and rate limiting
Attendance at this workshop is allocated on a first come, first served basis. Please complete the online application form to register.
Programme
Tuesday, 17th October 2023 19:00 - 17:00 (BST) | Overview of the REST API and how to query the REST API with URLs Fetching REST endpoints programmatically |
Wednesday, 18th October 2023 19:00 - 12:00 (BST) | Fetching specific data points from REST queries Linking REST queries together |
Thursday, 20th October 2023 19:00 - 12:00 (BST) | Bulk REST API queries with POST Other data types and rate limiting |
Attendance at this workshop is allocated on a first come, first served basis. Please complete the online application form to register.