omophub-package: omophub: R Client for the OMOPHub Medical Vocabulary API

In omophub: R Client for the 'OMOPHub' Medical Vocabulary API

omophub: R Client for the OMOPHub Medical Vocabulary API

Description

Provides an R interface to the OMOPHub API for accessing OHDSI ATHENA standardized medical vocabularies. Supports concept search, vocabulary exploration, hierarchy navigation, relationship queries, and concept mappings with automatic pagination and rate limiting.

Provides an R interface to the OMOPHub API for accessing OHDSI ATHENA standardized medical vocabularies. Supports concept search, vocabulary exploration, hierarchy navigation, relationship queries, and concept mappings with automatic pagination and rate limiting.

Main Client

The main entry point is the OMOPHubClient R6 class which provides access to all API resources:

library(omophub)
client <- OMOPHubClient$new()

# Search for concepts
results <- client$search$basic("diabetes")

# Get a specific concept
concept <- client$concepts$get(201826)

Authentication

Set your API key using one of these methods:

• Environment variable: OMOPHUB_API_KEY

• Explicit argument: OMOPHubClient$new(api_key = "your_key")

• Keyring: set_api_key("your_key", store = "keyring")

Resources

The client provides access to these resources:

• concepts: Concept lookup and batch operations

• search: Basic and advanced concept search

• vocabularies: Vocabulary listing and details

• domains: Domain listing and concept filtering

• hierarchy: Ancestor and descendant navigation

• relationships: Concept relationships

• mappings: Concept mappings between vocabularies

Author(s)

Maintainer: OMOPHub Team [e-mail] [copyright holder]

See Also

Useful links:

• https://github.com/omopHub/omophub-R

• https://docs.omophub.com

• Report bugs at https://github.com/omopHub/omophub-R/issues

omophub documentation built on Dec. 17, 2025, 5:10 p.m.