Get taxonomy metadata

Get the taxonomy report using scientific name

datasets summary taxonomy taxon "rattus norvegicus"

Get the names report using NCBI taxonomic ID

datasets summary taxonomy taxon 10114 --report names

Download a taxonomy data package that includes all taxonomic children

datasets download taxonomy taxon 33554 --children

In addition to the taxonomy report, the taxonomy data package includes a TSV file (taxonomy_summary.tsv) with the following fields:

Taxid
Tax name
Authority
Rank
Basionym
Basionym authority
Curator common name
Has type material
Group name
Superkingdom name
Superkingdom taxid
Kingdom name
Kingdom taxid
Phylum name
Phylum taxid
Class name
Class taxid
Order name
Order taxid
Family name
Family taxid
Genus name
Genus taxid
Species name
Species taxid

Get the taxonomy_summary.tsv file using datasets and dataformat

Rather than downloading a package that contains the taxonomy summary table, you can print the table to the screen:

datasets summary taxonomy taxon 9606 --as-json-lines | dataformat tsv taxonomy --template tax-summary
Taxid    Tax name    Authority    Rank    Basionym    Basionym authority    Curator common name    Has type material    Group name    Superkingdom nameSuperkingdom taxid    Kingdom name    Kingdom taxid    Phylum name    Phylum taxid    Class name    Class taxid    Order name    Order taxid    Family name    Family taxid    Genus name    Genus taxid    Species name    Species taxid
9606    Homo sapiens    Linnaeus, 1758    SPECIES            human    no    primates    Eukaryota    2759    Metazoa    33208    Chordata    7711    Mammalia    40674    Primates    9443    Hominidae    9604    Homo    9605    Homo sapiens    9606 

Note: Always use --as-json-lines when piping data from datasets to dataformat

Related information

• NCBI Datasets Taxonomy Data Package