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The Ensembl REST API: Ensembl Data for Any Language.

Andrew Yates1, Kathryn Beal1, Stephen Keenan1

  • 1European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

Bioinformatics (Oxford, England)
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PubMed
Summary
This summary is machine-generated.

This study introduces a new Ensembl RESTful web service for easy access to Ensembl data. It supports large-scale variant analysis through the Variant Effect Predictor tool.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Web Services

Background:

  • Ensembl provides a vast repository of genomic data.
  • Programmatic access to Ensembl data is crucial for large-scale analysis.
  • Existing methods for data retrieval can be cumbersome.

Purpose of the Study:

  • To develop a user-friendly web service for accessing Ensembl data.
  • To facilitate programmatic retrieval of diverse Ensembl datasets.
  • To enable large-scale variant analysis using Ensembl resources.

Main Methods:

  • Implementation of a Representational State Transfer (REST) web service.
  • Support for standard data formats like JSON and FASTA.
  • Integration with the Ensembl Variant Effect Predictor tool for programmatic analysis.

Main Results:

  • The Ensembl REST server allows easy data retrieval across multiple programming languages.
  • Minimized client-side workload for data access.
  • Enabled large-scale, language-independent variant analysis.

Conclusions:

  • The Ensembl REST API offers an efficient solution for accessing genomic data.
  • The integration with Variant Effect Predictor enhances programmatic variant analysis capabilities.
  • This service simplifies complex bioinformatics workflows.