taxonomy: Download taxonomy database.

In insect: Informatic Sequence Classification Trees

Description

This function downloads an up-to-date copy of the taxonomy database.

Usage

taxonomy(db = "NCBI", synonyms = FALSE)

Arguments

db	character string specifying which taxonomy database to download. Currently only "NCBI" is supported.
synonyms	logical indicating whether synonyms should be included. Note that this increases the size of the returned object by around 10%.

Details

This function downloads the specified taxonomy database as a data.frame object with the following columns: "taxID", "parent_taxID", "rank", "name". As of early 2018 the zip archive to download the NCBI taxonomy database is approximately 40Mb in size, and the output dataframe object is around 200Mb in memory. Once downloaded, the dataframe can be pruned for increased speed and memory efficiency using the function prune_taxonomy.

Value

a dataframe with the following elements: "taxID", "parent_taxID", "rank", "name".

Author(s)

Shaun Wilkinson

References

Federhen S (2012) The NCBI Taxonomy database. Nucleic Acids Research 40, D136-D143. doi:10.1093/nar/gkr1178.

https://www.ncbi.nlm.nih.gov/taxonomy/

Examples

  # db <- taxonomy()

insect documentation built on Aug. 9, 2021, 5:07 p.m.