In PatrickRWright/ATCapiR: An R Package to Query the NCBO Bioportal ATC Code API

ATCapiR r badger::badge_custom("dev version", as.character(packageVersion("ATCapiR")), "blue", "https://github.com/PatrickRWright/ATCapiR")

Before you install

If you would like to work with this package you will first need to create a personal account at the NCBI Bioportal. Withing your account information you should be able to find an API key. Only a valid API key will allow you to use the package.

Installing from GitHub with devtools

devtools::install_github("PatrickRWright/ATCapiR")

Basic usage

# load the package
library(ATCapiR)
# vector of ATC codes
ATC_vect <- c("A02BC02", "C03BA08", "A02BC02", "A02BC02", "A07DA03", "A07DA03",
              "A02BC02", "A02BC02", "A02BC02", "A02BC02", "C10AA05", "C10AA05",
              "C10AA05", "N05BA06", "N05BA06", "N05BA06", "N06AX11", "N06AX11")
# you will need to create an account at https://bioportal.bioontology.org/ to receive an api_key
# the key below is not real and just supposed to give you an impression of the format
api_key <- "a123b456-cd78-91e2-fgh3-4ij56kl7mno8"
# return translation at third level resolution
ATC_translated_df <- translate_ATC_codes(ATC_vect, level_depth = 3, api_key = api_key)

If HTTP error 401 is returned your API key is likely wrong or void.

PatrickRWright/ATCapiR documentation built on Jan. 27, 2021, 3:30 a.m.