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ncbi_taxonomy — NCBI Taxonomy (2014-2026)

Description

Networks of the NCBI Taxonomy, the taxonomic classification of all the organisms with sequences in the public sequence databases of the International Nucleotide Sequence Database Collaboration (GenBank, ENA, DDBJ), curated by the National Center for Biotechnology Information, which is the reference taxonomy of most biological databases. Besides species and higher taxa, it contains strains, isolates, environmental samples and unclassified organisms.

Nodes are taxa, and a directed edge goes from each taxon to its parent taxon, so that the networks are trees, rooted at the taxon root (tax_id 1), whose parent is itself in the data (this self-loop is left out).

There is one network for each year from 2014 to 2026, from the last monthly taxonomy dump of the year in the archive of the NCBI (which starts in August 2014): December 1 of each year from 2014 to 2025, and October 1, 2026 (the latest one).

The networks have the following properties:

  • (Node) tax_id: the identifier of the taxon.
  • (Node) name: the scientific name of the taxon.
  • (Node) common_name: the GenBank common name of the taxon (or another common name; empty if it has none).
  • (Node) rank: the rank of the taxon (e.g. species, genus, family, strain, no rank).
  • (Node) division: the GenBank division of the taxon (e.g. Bacteria, Invertebrates, Primates, Viruses).
  • (Node) genetic_code, mito_genetic_code: the identifiers of the genetic code and of the mitochondrial genetic code of the taxon.
  • (Node) is_hidden: whether the taxon is hidden in the lineages shown in GenBank entries.
Tags
Biological Informational Unweighted Tree Metadata
Added
2026-10-31
Citation
  • C. L. Schoch, S. Ciufo, M. Domrachev, C. L. Hotton, S. Kannan, R. Khovanskaya, D. Leipe, R. Mcveigh, K. O'Neill, B. Robbertse, S. Sharma, V. Soussov, J. P. Sullivan, L. Sun, S. Turner, I. Karsch-Mizrachi, "NCBI Taxonomy: a comprehensive update on curation, resources and tools." Database 2020, baaa062 (2020) 10.1093/database/baaa062 Sci-Hub
Upstream URL OK
https://www.ncbi.nlm.nih.gov/taxonomy
https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/
Upstream license
Public domain (NCBI data), https://www.ncbi.nlm.nih.gov/home/about/policies/
Networks
Tip: click on a column header to sort the list, or hover over it for a description.
Column legend
$\left<k\right>$
Mean degree
$\sigma_k$
Standard deviation of the degrees
$\lambda_h$
Largest eigenvalue of the Hashimoto (non-backtracking) matrix
$\tau$
Random walk mixing time
$r$
Degree assortativity
$c$
Global clustering coefficient
$\oslash$
(Pseudo-) diameter
$S$
Relative size of the largest component
NPs
Node properties
EPs
Edge properties
Name Nodes Edges $\left<k\right>$ $\sigma_k$ $\lambda_h$ $\tau$ $r$ $c$ $\oslash$ $S$ Kind Mode NPs EPs gt GraphML GML csv
2014 1,226,376 1,226,375 1.00 71.18 1.00 1309366.30 -0.11 0.00 62 1.00 Directed Bipartite tax_id name common_name rank division genetic_code mito_genetic_code is_hidden 9.7 MiB 16.9 MiB 16.1 MiB 19.8 MiB
2015 1,387,306 1,387,305 1.00 74.85 1.00 12294509.75 -0.12 0.00 62 1.00 Directed Bipartite tax_id name common_name rank division genetic_code mito_genetic_code is_hidden 10.9 MiB 18.9 MiB 18.1 MiB 22.3 MiB
2016 1,537,566 1,537,565 1.00 76.34 1.00 1668064.49 -0.12 0.00 61 1.00 Directed Bipartite tax_id name common_name rank division genetic_code mito_genetic_code is_hidden 12.0 MiB 21.0 MiB 19.9 MiB 24.7 MiB
2017 1,661,917 1,661,916 1.00 77.09 1.00 6001524.41 -0.12 0.00 61 1.00 Directed Bipartite tax_id name common_name rank division genetic_code mito_genetic_code is_hidden 12.9 MiB 22.5 MiB 21.5 MiB 26.7 MiB
2018 2,033,846 2,033,845 1.00 78.96 1.00 13119231.43 -0.12 0.00 61 1.00 Directed Bipartite tax_id name common_name rank division genetic_code mito_genetic_code is_hidden 14.9 MiB 26.6 MiB 25.5 MiB 31.6 MiB
2019 2,192,179 2,192,178 1.00 77.23 1.00 3836493.49 -0.11 0.00 61 1.00 Directed Bipartite tax_id name common_name rank division genetic_code mito_genetic_code is_hidden 16.3 MiB 29.0 MiB 27.8 MiB 34.4 MiB
2020 2,293,084 2,293,083 1.00 76.17 1.00 6555252.26 -0.11 0.00 61 1.00 Directed Bipartite tax_id name common_name rank division genetic_code mito_genetic_code is_hidden 17.2 MiB 30.5 MiB 29.1 MiB 36.1 MiB
2021 2,383,917 2,383,916 1.00 75.12 1.00 1364419.12 -0.11 0.00 61 1.00 Directed Bipartite tax_id name common_name rank division genetic_code mito_genetic_code is_hidden 17.9 MiB 31.8 MiB 30.5 MiB 37.7 MiB
2022 2,471,146 2,471,145 1.00 74.16 1.00 23716322.17 -0.10 0.00 62 1.00 Directed Bipartite tax_id name common_name rank division genetic_code mito_genetic_code is_hidden 18.8 MiB 33.2 MiB 31.9 MiB 39.2 MiB
2023 2,544,505 2,544,504 1.00 73.65 1.00 11301615.17 -0.10 0.00 62 1.00 Directed Bipartite tax_id name common_name rank division genetic_code mito_genetic_code is_hidden 19.5 MiB 34.3 MiB 32.9 MiB 40.6 MiB
2024 2,631,604 2,631,603 1.00 73.53 1.00 1824925.34 -0.10 0.00 63 1.00 Directed Bipartite tax_id name common_name rank division genetic_code mito_genetic_code is_hidden 20.1 MiB 35.6 MiB 34.2 MiB 42.0 MiB
2025 2,708,758 2,708,757 1.00 72.97 1.00 1814768.01 -0.10 0.00 63 1.00 Directed Bipartite tax_id name common_name rank division genetic_code mito_genetic_code is_hidden 20.9 MiB 36.9 MiB 35.3 MiB 43.4 MiB
2026 3,016,750 3,016,749 1.00 71.61 1.00 2085073.61 -0.09 0.00 67 1.00 Directed Bipartite tax_id name common_name rank division genetic_code mito_genetic_code is_hidden 23.0 MiB 40.7 MiB 39.1 MiB 48.0 MiB