The NCBI Taxonomy database

TLDR

The NCBI Taxonomy database is the standard nomenclature and classification repository for the International Nucleotide Sequence Database Collaboration, providing organism names, taxonomic lineages, and serving as a central hub for linking NCBI resources. The database aims to index sequence domains in a user‑friendly manner for the community. A small NCBI team manually curates the taxonomy using current literature to maintain a phylogenetic classification of source organisms.

Abstract

The NCBI Taxonomy database (http://www.ncbi.nlm.nih.gov/taxonomy) is the standard nomenclature and classification repository for the International Nucleotide Sequence Database Collaboration (INSDC), comprising the GenBank, ENA (EMBL) and DDBJ databases. It includes organism names and taxonomic lineages for each of the sequences represented in the INSDC’s nucleotide and protein sequence databases. The taxonomy database is manually curated by a small group of scientists at the NCBI who use the current taxonomic literature to maintain a phylogenetic taxonomy for the source organisms represented in the sequence databases. The taxonomy database is a central organizing hub for many of the resources at the NCBI, and provides a means for clustering elements within other domains of NCBI web site, for internal linking between domains of the Entrez system and for linking out to taxon-specific external resources on the web. Our primary purpose is to index the domain of sequences as conveniently as possible for our user community.