In mpancia/rUMLS: An R Interface To The NLM Unified Medical Language System

Introduction

rUMLS is an interface to the National Library of Medicine's Unified Medicial Language System. The UMLS provides a way of linking many disparate medical vocabularies into a single graph, allowing for the unification of concepts and relations across these vocabularies.

There are several ways of accessing the UMLS:

The web interface provided by the NLM;
The REST API;
The SOAP API;
A download of the underlying data, which allows for the creation of SQL load scripts.

The goal of this package is to provide an abstracted interface to the REST API provided by the NLM, making it easy to search for concepts, access relationships, and get other information like synonyms/translations/etc. Eventually, plotting tools and helper functions to understand the graphical structure will be added.

Authentication

This package requires a UMLS license, which includes user credentials. By using this package, you are subject to the licensing agreements that you agree to with the NLM.

You can authenticate with the UMLS on a per-session basis using the auth_UMLS() function, but it is easier to include the relevant credentials in your .Renviron file located in your home directory. Add the following lines to your file:

UMLS_USER=<username>
UMLS_PASS=<password>

Once these are set, auth_UMLS() will load your credentials and authenticate you with the UMLS. If you wish to reset your credentials, use the umls_creds() function.