R: NCBI taxon information from uids

ncbi_get_taxon_summary {taxize}

R Documentation

NCBI taxon information from uids

Description

Downloads summary taxon information from the NCBI taxonomy databases for a set of taxonomy UIDs using eutils esummary.

Usage

ncbi_get_taxon_summary(id, key = NULL, ...)

Arguments

`id`	(character) NCBI taxonomy uids to retrieve information for. See Details.
`key`	(character) NCBI Entrez API key. optional. See Details.
`...`	Curl options passed on to `HttpClient`

Details

If your input vector or list of NCBI IDs is longer than about 8000 characters (use nchar(paste(ids, collapse = "+"))), split the list up into chunks since at about that number of characters you will run into the HTTP 414 error "Request-URI Too Long".

Value

A data.frame with the following columns:

uid: The uid queried for
name: The name of the taxon; a binomial name if the taxon is of rank species
rank: The taxonomic rank (e.g. 'Genus')

Authentication

See taxize-authentication for help on authentication

Author(s)

Zachary Foster zacharyfoster1989@Sgmail.com

Examples

## Not run: 
ncbi_get_taxon_summary(c(1430660, 4751))

# use curl options
ncbi_get_taxon_summary(c(1430660, 4751), verbose = TRUE)

## End(Not run)

[Package taxize version 0.9.3 Index]