taxon

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
      --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 Taxons 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