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 Vocabularies
Get a paginated list of all available medical vocabularies:
# Basic list
result <- client$vocabularies$list()
for (vocab in result$data$vocabularies) {
cat(sprintf("%s: %s\n", vocab$vocabulary_id, vocab$vocabulary_name))
}
# Include statistics
result <- client$vocabularies$list(include_stats = TRUE)
for (vocab in result$data$vocabularies) {
cat(sprintf("%s: %s concepts\n", vocab$vocabulary_id, vocab$concept_count))
}
# Custom sorting and pagination
result <- client$vocabularies$list(
sort_by = "name",
sort_order = "asc",
page = 1,
page_size = 50
)
Parameters
| Parameter | Type | Default | Description |
|---|
include_stats | logical | FALSE | Include vocabulary statistics |
include_inactive | logical | FALSE | Include inactive vocabularies |
sort_by | character | ”name” | Sort field (“name”, “priority”, “updated”) |
sort_order | character | ”asc” | Sort order (“asc”, “desc”) |
page | integer | 1 | Page number |
page_size | integer | 100 | Results per page (max 1000) |
Get Vocabulary Details
Get detailed information about a specific vocabulary:
vocab <- client$vocabularies$get("SNOMED")
cat(sprintf("Name: %s\n", vocab$data$vocabulary_name))
cat(sprintf("Version: %s\n", vocab$data$vocabulary_version))
cat(sprintf("Reference: %s\n", vocab$data$vocabulary_reference))
Parameters
| Parameter | Type | Default | Description |
|---|
vocabulary_id | character | required | Vocabulary identifier (e.g., “SNOMED”, “ICD10CM”) |
Response Fields
Returns vocabulary_id, vocabulary_name, vocabulary_reference, vocabulary_version, vocabulary_concept_id.
For detailed statistics, use client$vocabularies$stats(vocabulary_id).
Get Vocabulary Statistics
Get statistical information about a vocabulary:
stats <- client$vocabularies$stats("SNOMED")
cat(sprintf("Total concepts: %d\n", stats$total_concepts))
cat(sprintf("Standard concepts: %d\n", stats$standard_concepts))
Get Domain Statistics
Get statistics for a specific domain within a vocabulary:
result <- client$vocabularies$domain_stats("SNOMED", "Condition")
cat(sprintf("Total concepts: %d\n", result$data$total_concepts))
cat(sprintf("Standard concepts: %d\n", result$data$standard_concepts))
# View concept class breakdown
for (cls in result$data$concept_classes) {
cat(sprintf("%s: %d concepts\n", cls$concept_class_id, cls$concept_count))
}
Parameters
| Parameter | Type | Default | Description |
|---|
vocabulary_id | character | required | Vocabulary identifier (e.g., “SNOMED”, “ICD10CM”) |
domain_id | character | required | Domain identifier (e.g., “Condition”, “Drug”, “Procedure”) |
Get Vocabulary Domains
Get all standard OHDSI domains:
result <- client$vocabularies$domains()
for (domain in result$data$domains) {
cat(sprintf("%s: %s\n", domain$domain_id, domain$domain_name))
}
domain_id, domain_name, and description.
Get Concept Classes
Get all available concept classes:
result <- client$vocabularies$concept_classes()
for (cls in result$data) {
cat(sprintf("%s: %s\n", cls$concept_class_id, cls$concept_class_name))
}
concept_class_id, concept_class_name, and concept_class_concept_id.
Get Vocabulary Concepts
Retrieve concepts within a specific vocabulary with filtering and pagination:
# Basic usage
result <- client$vocabularies$concepts("SNOMED", page_size = 100)
for (concept in result$data$concepts) {
cat(sprintf("%s (%d)\n", concept$concept_name, concept$concept_id))
}
# Search within vocabulary
result <- client$vocabularies$concepts(
"SNOMED",
search = "diabetes",
standard_concept = "S",
page_size = 50
)
# Include additional data
result <- client$vocabularies$concepts(
"SNOMED",
search = "hypertension",
include_relationships = TRUE,
include_synonyms = TRUE
)
# With sorting
result <- client$vocabularies$concepts(
"RxNorm",
sort_by = "concept_id",
sort_order = "desc",
page_size = 100
)
# Include invalid/deprecated concepts
result <- client$vocabularies$concepts(
"ICD10CM",
include_invalid = TRUE,
page = 1,
page_size = 50
)
# Pagination
cat(sprintf("Page %d of %d\n",
result$meta$pagination$page,
result$meta$pagination$total_pages
))
cat(sprintf("Total: %d concepts\n", result$meta$pagination$total_items))
Parameters
| Parameter | Type | Default | Description |
|---|
vocabulary_id | character | required | Vocabulary identifier (e.g., “SNOMED”, “ICD10CM”) |
search | character | NULL | Search term to filter concepts by name or code |
standard_concept | character | ”all” | Filter by standard concept status (“S”, “C”, “all”) |
include_invalid | logical | TRUE | Include invalid or deprecated concepts |
include_relationships | logical | FALSE | Include concept relationships in response |
include_synonyms | logical | FALSE | Include concept synonyms in response |
sort_by | character | ”name” | Sort field (“name”, “concept_id”, “concept_code”) |
sort_order | character | ”asc” | Sort order (“asc”, “desc”) |
page | integer | 1 | Page number |
page_size | integer | 20 | Results per page (max 1000) |
