NCBI Taxonomy

Identifier

ncbi_taxonomy

License

Public domain

Citation

Schoch CL, Ciufo S, Domrachev M, et al. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database (Oxford). 2020;2020:baaa062. doi:10.1093/database/baaa062.

Overview

NCBI Taxonomy is NCBI’s curated classification of organisms and viruses.

This namespace contains taxon names, the parent-child hierarchy, lineages, genetic codes, type material, hosts, citations, and related taxonomy metadata.

names resolves organism names to taxon IDs, and nodes supplies each taxon’s immediate parent and rank. ranked_lineages, full_name_lineages, and taxon_id_lineages provide lineage paths.

Taxonomy IDs are opaque strings even when their values look numeric.

Tables

• ncbi_taxonomy.categories — NCBI’s broad category and species-level mapping, one row per taxon.
• ncbi_taxonomy.citations — Literature citations associated with NCBI Taxonomy nodes, one row per citation.
• ncbi_taxonomy.deleted_nodes — Deleted NCBI Taxonomy nodes, one row per deleted taxon ID.
• ncbi_taxonomy.divisions — NCBI Taxonomy divisions used by taxonomy nodes, one row per division.
• ncbi_taxonomy.full_name_lineages — Full NCBI Taxonomy name lineages, one row per taxon.
• ncbi_taxonomy.genetic_codes — NCBI genetic code definitions used by taxonomy nodes, one row per genetic code.
• ncbi_taxonomy.hosts — Theoretical hosts reported by NCBI for taxonomy nodes, one row per taxon.
• ncbi_taxonomy.images — Images associated with NCBI Taxonomy nodes, one row per image.
• ncbi_taxonomy.merged_nodes — NCBI Taxonomy nodes merged into replacement nodes, one row per superseded taxon ID.
• ncbi_taxonomy.names — Scientific names, synonyms, common names, and other NCBI Taxonomy names, one row per taxon name and name class.
• ncbi_taxonomy.nodes — NCBI Taxonomy node hierarchy and inherited classification settings, one row per taxon.
• ncbi_taxonomy.ranked_lineages — Selected NCBI Taxonomy ancestor names at established taxonomic ranks, one row per taxon.
• ncbi_taxonomy.taxon_id_lineages — Full NCBI Taxonomy ID lineages, one row per taxon.
• ncbi_taxonomy.type_material_exclusions — Strains and vouchers NCBI determined are not verified type material, one row per excluded record.
• ncbi_taxonomy.type_material_types — NCBI type material category definitions, one row per type material category.
• ncbi_taxonomy.type_materials — NCBI type material collection records associated with taxonomy nodes, one row per record.