NCBI Taxonomy: enhanced access via NCBI Datasets
Eric Cox, Mirian T. N. Tsuchiya, Stacy Ciufo, John Torcivia, Robert Falk, WF Anderson, J. Bradley Holmes, Vichet Hem, Laurie Breen, Emily Davis, Anne Ketter, Peifen Zhang, Vladimir Soussov, Conrad L. Schoch, Nuala A. O’Leary
Abstract
The NCBI Taxonomy resource (https://www.ncbi.nlm.nih.gov/taxonomy) has long been a trusted, curated hub for organism names, classifications, and links to related data for all taxonomic nodes. NCBI Datasets (https://www.ncbi.nlm.nih.gov/datasets/) is an improved way to leverage the rich data available at NCBI so users can effectively browse, search, and download information. While taxonomy data has been a cornerstone of NCBI Datasets since its inception, we recently extended the taxonomy information available via NCBI Datasets by updating the existing NCBI Datasets taxonomy page, implementing a new taxonomy name details page, expanding programmatic access to taxonomic information via command-line tools and APIs and improving the way we handle taxonomic queries to connect users to gene and genome data. This paper highlights these improvements and provides examples to help users effectively harness these new features.