BOLDconnectR: An R package for streamlined retrieval, transformation, and analysis of DNA barcode data on BOLD.

Abstract

DNA barcode data are essential infrastructure for biodiversity science as they enable scalable species identification and integrative analyses that link sequences to specimens, taxonomy, and geography. The Barcode of Life Data System (BOLD) is a centralized bioinformatics workbench that supports the full barcode data lifecycle: including acquisition, storage, validation, analysis, and dataset publication within a secure collaboration model. While BOLD's web interface is optimized for interactive dataset assembly and publication, many researchers require programmatic access to both public data and permissioned private records to build reproducible pipelines for curation and analysis prior to release. We introduce BOLDconnectR, an R package that provides authenticated access to BOLD, returns records in the Barcode Core Data Model (BCDM), performs automated transformation into commonly used R data structures, and enables customizable analytic workflows that generate publication-ready outputs.