Documentation Index
Fetch the complete documentation index at: https://docs.omophub.com/llms.txt
Use this file to discover all available pages before exploring further.
List All Domains
Get a list of all available OMOP domains:
# Basic list
result <- client$domains$list()
for (domain in result$data$domains) {
print(domain$domain_id)
}
# Include concept counts and statistics
result <- client$domains$list(include_stats = TRUE)
for (domain in result$data$domains) {
cat(sprintf("%s: %d concepts\n", domain$domain_id, domain$concept_count))
}
Get Domain Concepts
Retrieve all concepts within a specific domain:
# Basic usage
result <- client$domains$concepts("Condition", page_size = 100)
for (concept in result$data$concepts) {
cat(sprintf("%s (%d)\n", concept$concept_name, concept$concept_id))
}
# Filter by vocabulary
result <- client$domains$concepts(
"Condition",
vocabulary_ids = c("SNOMED", "ICD10CM"),
page_size = 50
)
# Standard concepts only
result <- client$domains$concepts(
"Drug",
vocabulary_ids = "RxNorm",
standard_only = TRUE,
page_size = 100
)
# Include invalid/deprecated concepts
result <- client$domains$concepts(
"Procedure",
include_invalid = TRUE,
page = 1,
page_size = 50
)
# Pagination
cat(sprintf("Page %d of %d\n",
result$meta$pagination$page,
result$meta$pagination$total_pages
))
cat(sprintf("Total: %d concepts\n", result$meta$pagination$total_items))
Parameters
| Parameter | Type | Default | Description |
|---|
domain_id | character | required | Domain identifier (e.g., “Condition”, “Drug”) |
vocabulary_ids | character | NULL | Filter to specific vocabularies |
standard_only | logical | FALSE | Return only standard concepts |
include_invalid | logical | TRUE | Include deprecated concepts |
page | integer | 1 | Page number |
page_size | integer | 50 | Results per page (max 1000) |