NCBI taxon information from uids

Source: R/ncbi_get_taxon_summary.R

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

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 crul::verb-GET

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')

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".

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 zacharyfoster1989@Sgmail.com

Examples

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

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