taxize (version 0.9.100.1)

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, ...)

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')

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 crul::verb-GET

HTTP version

We hard code http_version = 2L to use HTTP/1.1 in HTTP requests to the Entrez API. See curl::curl_symbols('CURL_HTTP_VERSION')

Authentication

See taxize-authentication for help on authentication. We strongly recommend getting an API key

Author

Zachary Foster

Details

If your input vector or list of NCBI IDs is longer than about 2500 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

if (FALSE) {
ncbi_get_taxon_summary(c(1430660, 4751))

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