taxize (version 0.9.4)

ncbi_get_taxon_summary: 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

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

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".

Examples

# NOT RUN {
ncbi_get_taxon_summary(c(1430660, 4751))

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