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 hierarchy and associated nomenclature, lineage, type-material, host, image, and citation metadata from NCBI Taxonomy dump archives.

The rolling new_taxdump archive is verified against NCBI’s published MD5 checksum.

Its computed SHA-256 checksum and HTTP Last-Modified timestamp identify each ingestion. categories is sourced separately from the taxcat archive.

All identifiers, including numeric-looking NCBI taxonomy IDs, are opaque strings; numeric types are reserved for quantities.

Tables

• ncbi_taxonomy.categories — NCBI’s broad category and species-level mapping for each taxon, from categories.dmp in the taxcat archive.
• ncbi_taxonomy.citations — Literature citations associated with NCBI Taxonomy nodes, from citations.dmp.
• ncbi_taxonomy.deleted_nodes — Deleted NCBI Taxonomy nodes, from delnodes.dmp.
• ncbi_taxonomy.divisions — NCBI Taxonomy divisions used by taxonomy nodes, from division.dmp.
• ncbi_taxonomy.full_name_lineages — Full NCBI Taxonomy name lineages, from fullnamelineage.dmp.
• ncbi_taxonomy.genetic_codes — NCBI genetic code definitions used by taxonomy nodes, from gencode.dmp.
• ncbi_taxonomy.hosts — Theoretical hosts reported by NCBI for taxonomy nodes, from host.dmp.
• ncbi_taxonomy.images — Images associated with NCBI Taxonomy nodes, from images.dmp.
• ncbi_taxonomy.merged_nodes — NCBI Taxonomy nodes merged into replacement nodes, from merged.dmp.
• ncbi_taxonomy.names — Scientific names, synonyms, common names, and other NCBI Taxonomy names, from names.dmp.
• ncbi_taxonomy.nodes — NCBI Taxonomy node hierarchy and inherited classification settings, from nodes.dmp.
• ncbi_taxonomy.ranked_lineages — Selected NCBI Taxonomy ancestor names at established taxonomic ranks, from rankedlineage.dmp.
• ncbi_taxonomy.taxon_id_lineages — Full NCBI Taxonomy ID lineages, from taxidlineage.dmp.
• ncbi_taxonomy.type_material_exclusions — Strains and vouchers NCBI determined are not verified type material, from excludedfromtype.dmp.
• ncbi_taxonomy.type_material_types — NCBI type material category definitions, from typeoftype.dmp.
• ncbi_taxonomy.type_materials — NCBI type material collection records associated with taxonomy nodes, from typematerial.dmp.