taxonomy

Name

datasets download taxonomy - Download a taxonomy data package

Synopsis

datasets download taxonomy [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
      --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
      --no-progressbar    Hide progress bar
      --version           Print version of datasets

Commands