biomaRt, Comprehensive Skill Guide

Domain: Annotation / ID mapping Bioconductor: biomaRt Paper: Durinck S et al. (2009). Nature Protocols, 4:1184-1191.

Query Ensembl BioMart databases to retrieve gene annotations, ID conversions, sequence retrieval, and cross-species homology information.

Dependencies & Environment

Package-intrinsic requirements from the Bioconductor landing page, reproduce in any R environment.

• Version: 2.68.0 · Bioconductor: 3.23 · R: ≥ 4.6
• Imports: AnnotationDbi, BiocFileCache, curl, httr2, progress, stringr, xml2
• Install: BiocManager::install("biomaRt")

When to Use

• Convert between gene IDs (Ensembl → HGNC symbol → Entrez → RefSeq)
• Retrieve gene coordinates, GO terms, pathway annotations
• Get protein sequences or transcript sequences
• Cross-species homology / ortholog mapping

Alternatives: AnnotationDbi (OrgDb), AnnotationHub, mygene (Python/R)

Do NOT Use When

• Offline environments, biomaRt requires internet access to Ensembl servers.
• Very large ID lists (>100K IDs), consider AnnotationDbi local OrgDb instead for speed.
• Non-Ensembl databases without a BioMart interface.

Data Requirements

Requirement	Details
Internet	Required, queries Ensembl servers remotely
Notes	Cache results locally; pin Ensembl version for reproducibility

Installation

if (!require("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("biomaRt")
library(biomaRt)

Workflows

Gene ID Conversion (Ensembl → HGNC Symbol → Entrez)

Convert a list of Ensembl gene IDs to gene symbols and Entrez IDs

Connect to Ensembl

library(biomaRt)
ensembl <- useEnsembl(biomart="genes", dataset="hsapiens_gene_ensembl")

Check available attributes and filters