ncbi_get_taxon_summary: NCBI taxon information from uids

In taxize: Taxonomic Information from Around the Web

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 crul::verb-GET

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".

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')

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(s)

Zachary Foster [e-mail]

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)

taxize documentation built on Sept. 11, 2024, 6:13 p.m.