taxon

Download a taxonomy package by taxonomy taxon (NCBI Taxonomy ID, scientific or common name at any tax rank)

taxon

Download a taxonomy package by taxonomy taxon (NCBI Taxonomy ID, scientific or common name at any tax rank)

Name

datasets download taxonomy taxon - Download a taxonomy package by taxonomy taxon (NCBI Taxonomy ID, scientific or common name at any tax rank)

Synopsis

datasets download taxonomy taxon <taxon...> [flags]

Description

Download a taxonomy data package by taxonomy taxon (NCBI Taxonomy ID, scientific or common name at any tax rank).

The default taxonomy data package includes the following files:

  • taxonomy_report.jsonl
  • taxonomy_summary.tsv
  • dataset_catalog.json (a list of files and file types included in the data package) A taxonomy names data report can also be added to the package
  • names_report.jsonl

Examples

  datasets download taxonomy taxon "bos taurus"
  datasets download taxonomy taxon human,"drosophila melanogaster" --include names
  datasets download taxonomy taxon 10116 --parents --children

Options

      --api-key string        Specify an NCBI API key
      --children              Return all taxonomic children of the requested taxon
      --debug                 Emit debugging info
      --fast-zip-validation   Skip zip checksum validation after download
      --filename string       Specify a custom file name for the downloaded data package (default "ncbi_dataset.zip")
      --help                  Print detailed help about a datasets command
      --include string        Add report to download:
                                * names:          taxonomy names report
                                 (default "[]")
      --inputfile string      Read a list of NCBI taxonomy identifiers (taxid or current scientific name) from a file to use as input
      --no-progressbar        Hide progress bar
      --parents               Include all parents of the requested taxon
      --rank strings          Limit taxons to only those with the specified ranks. When enabled, the children and parents flags will be enabled as well.
      --version               Print version of datasets
Generated February 26, 2025