We have written an R package client to the Concept Library API, which allows you to connect and download content directly into data frames in R.

Downloading and installing the R package

External: the package is available on Github and can be installed using the install_github() function in devtools. This will automatically download and install dependencies, like installing from CRAN.

Using devtools to install ConceptLibraryClient from Github
install.packages("devtools");
library(devtools);

install_github("DSThayer/concept-library-client", subdir="ConceptLibraryClient");

Internal: the package is available with other packages we have developed for SAIL users, in R:/r_packages/ConceptLibraryClient. Please run the install.r script to install the package and dependencies.

Getting concepts into data frames

To bring content into R, first search the concept library for the concept you want and note its ID number. If you want to get a specific version of a concept, also note its version ID (if not specified, you will always get the latest version). Then use the commands below to retrieve concepts.


Getting concepts
library(ConceptLibraryClient);

#Retrieve the latest version of a concept. You will be prompted for a username and password
copd_icd10 = ConceptLibraryClient::get_concept_codes(
  url='https://conceptlibrary.saildatabank.com',
  id=141
);

#View the retrieved data frame
copd_icd10;

#Set your credentials so you don't have to log in for each command.
credentials = create_auth();

#Get a concept, explicitly specifying a particular version.
copd_icd10_20200602 = get_concept_codes(
  url='https://conceptlibrary.saildatabank.com',
  id=141,
  version=392,
  auth=credentials #Supply username and password
);

#Retrieve multiple concepts into a single data frame
comorbidities_primary_care = get_concept_codes(
  url='https://conceptlibrary.saildatabank.com',
  id=c(140,142,144),
  auth=credentials
);
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