ensembldb: an R package to create and use Ensembl-based annotation resources

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• Bioinformatics research often requires managing gene-centric data, including exons, transcripts, and proteins.
• Accurate positional information relative to a reference coordinate system is crucial for gene-associated data analysis.

Purpose of the Study:

• To introduce the ensembldb Bioconductor package for efficient retrieval and storage of Ensembl genetic annotations.
• To facilitate identifier conversion and coordinate mapping for gene-associated data.
• To support reproducible research by linking data to specific Ensembl releases.

Main Methods:

• Utilizes the Bioconductor framework for package development and distribution.
• Stores Ensembl genetic annotations and positional information.
• Provides functions for identifier mapping and coordinate transformation.
• Offers pre-made data packages for diverse genomes and Ensembl releases.

Main Results:

• The ensembldb package effectively retrieves and stores Ensembl genetic annotations.
• It enables seamless identifier conversion and coordinate mapping for gene-related data.
• Data are versioned according to Ensembl releases, ensuring reproducibility.
• Pre-built data packages are available for multiple genomes.

Conclusions:

• ensembldb is a valuable tool for bioinformatics, simplifying the handling of gene-centric data.
• Its design promotes reproducible research through release-specific data management.
• The package enhances gene annotation and coordinate mapping workflows.