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.
Get a Concept
Retrieve a concept by its OMOP concept ID:
concept <- client$concepts$get(201826)
print(concept$concept_name) # "Type 2 diabetes mellitus"
print(concept$vocabulary_id) # "SNOMED"
print(concept$domain_id) # "Condition"
Get by Vocabulary Code
Look up a concept using a vocabulary-specific code:
# Get SNOMED concept by its code
concept <- client$concepts$get_by_code("SNOMED", "44054006")
print(concept$concept_name) # "Type 2 diabetes mellitus"
# Get ICD-10-CM concept
concept <- client$concepts$get_by_code("ICD10CM", "E11")
# Include synonyms and relationships
concept <- client$concepts$get_by_code(
"SNOMED",
"44054006",
include_synonyms = TRUE,
include_relationships = TRUE
)
print(concept$synonyms) # List of synonym names
print(concept$relationships) # list(parents = [...], children = [...])
# Specify vocabulary release version
concept <- client$concepts$get_by_code(
"SNOMED",
"44054006",
vocab_release = "2025.2"
)
Batch Get Concepts
Retrieve multiple concepts in a single request (max 100):
# Basic batch request
result <- client$concepts$batch(c(201826, 4329847, 1112807))
for (concept in result$data$concepts) {
cat(sprintf("%s: %s\n", concept$concept_id, concept$concept_name))
}
# With optional parameters
result <- client$concepts$batch(
c(201826, 4329847, 1112807),
include_relationships = TRUE,
include_synonyms = TRUE,
include_mappings = TRUE,
vocabulary_filter = c("SNOMED"),
standard_only = FALSE # default
)
# Check summary
cat(sprintf("Retrieved: %d\n", result$data$summary$successful_retrievals))
cat(sprintf("Failed: %d\n", result$data$summary$failed_retrievals))
Autocomplete Suggestions
Get concept suggestions for autocomplete functionality:
# Basic suggestions with pagination
result <- client$concepts$suggest("diab", page_size = 10)
for (concept in result$data) {
print(concept$concept_name)
}
# Check pagination metadata
print(result$meta$pagination$total_items)
print(result$meta$pagination$has_next)
# Filter by vocabulary and domain
result <- client$concepts$suggest(
"diab",
vocabulary_ids = c("SNOMED"),
domain_ids = c("Condition"),
page_size = 20
)
# Navigate pages
result <- client$concepts$suggest("diab", page = 2, page_size = 10)
Get Relationships
Get relationships for a concept:
# Get all relationships with pagination
result <- client$relationships$get(201826)
for (rel in result$data$relationships) {
cat(sprintf("%s: %s\n", rel$relationship_id, rel$concept_2$concept_name))
}
# Check pagination
cat(sprintf("Page %d of %d\n",
result$meta$pagination$page,
result$meta$pagination$total_pages
))
cat(sprintf("Total relationships: %d\n", result$meta$pagination$total_items))
# Filter by relationship type and vocabulary
result <- client$relationships$get(
201826,
relationship_ids = c("Is a", "Subsumes"),
vocabulary_ids = "SNOMED",
standard_only = TRUE,
page = 1,
page_size = 50
)
# Include reverse relationships
result <- client$relationships$get(
201826,
include_reverse = TRUE,
domain_ids = c("Condition")
)
Navigate Hierarchy
Get Complete Hierarchy
Get both ancestors and descendants in a single request:
# Flat format (default) - separate arrays for ancestors and descendants
result <- client$hierarchy$get(
201826,
max_levels = 3,
vocabulary_ids = c("SNOMED")
)
cat(sprintf("Total ancestors: %d\n", result$data$total_ancestors))
cat(sprintf("Total descendants: %d\n", result$data$total_descendants))
# Graph format for visualization (D3.js, Cytoscape, etc.)
graph <- client$hierarchy$get(
201826,
format = "graph",
max_levels = 3
)
nodes <- graph$data$nodes # Concept nodes
edges <- graph$data$edges # Relationship edges
cat(sprintf("Nodes: %d, Edges: %d\n", length(nodes), length(edges)))
# Advanced filtering options
result <- client$hierarchy$get(
201826,
domain_ids = c("Condition"),
relationship_types = c("Is a"),
max_results = 100,
include_invalid = FALSE
)
Hierarchy Get Parameters
| Parameter | Type | Default | Description |
|---|
concept_id | integer | required | The concept ID |
format | character | ”flat” | Response format (“flat” or “graph”) |
vocabulary_ids | character | NULL | Filter to specific vocabularies |
domain_ids | character | NULL | Filter to specific domains |
max_levels | integer | 10 | Maximum hierarchy levels (max 20) |
max_results | integer | NULL | Maximum results per direction |
relationship_types | character | NULL | Relationship types to follow |
include_invalid | logical | TRUE | Include deprecated/invalid concepts |
Get Ancestors
Find parent concepts in the hierarchy:
result <- client$hierarchy$ancestors(
201826,
max_levels = 3,
vocabulary_ids = c("SNOMED"), # Filter to specific vocabularies
relationship_types = c("Is a"), # Relationship types to follow
include_distance = TRUE, # Include hierarchy_level field
include_paths = FALSE, # Include path information
include_invalid = FALSE, # Exclude deprecated concepts
page = 1,
page_size = 100
)
# Access source concept info
cat(sprintf("Ancestors of: %s\n", result$concept_name))
# Access ancestors
for (ancestor in result$ancestors) {
level <- ancestor$hierarchy_level %||% 0
cat(sprintf("%s%s\n", strrep(" ", level), ancestor$concept_name))
}
# Access hierarchy summary
cat(sprintf("Max depth: %d\n", result$hierarchy_summary$max_hierarchy_depth))
# Access pagination
cat(sprintf("Page %d of %d\n",
result$meta$pagination$page,
result$meta$pagination$total_pages
))
Ancestors Parameters
| Parameter | Type | Default | Description |
|---|
concept_id | integer | required | The concept ID |
vocabulary_ids | character | NULL | Filter to specific vocabularies |
max_levels | integer | NULL | Maximum hierarchy levels to traverse |
relationship_types | character | NULL | Relationship types to follow (default: “Is a”) |
include_paths | logical | FALSE | Include path information |
include_distance | logical | TRUE | Include hierarchy_level field |
include_invalid | logical | TRUE | Include deprecated/invalid concepts |
page | integer | 1 | Page number |
page_size | integer | 100 | Results per page |
Get Descendants
Find child concepts in the hierarchy:
result <- client$hierarchy$descendants(
201826,
max_levels = 2,
vocabulary_ids = c("SNOMED"), # Filter to specific vocabularies
relationship_types = c("Is a"), # Relationship types to follow
include_distance = TRUE, # Include hierarchy_level field
include_paths = FALSE, # Include path information
include_invalid = FALSE, # Exclude deprecated concepts
domain_ids = c("Condition"), # Filter by domain
page = 1,
page_size = 100
)
# Access descendants
for (descendant in result$descendants) {
print(descendant$concept_name)
}
# Access pagination
cat(sprintf("Page %d of %d\n",
result$meta$pagination$page,
result$meta$pagination$total_pages
))
Descendants Parameters
| Parameter | Type | Default | Description |
|---|
concept_id | integer | required | The concept ID |
vocabulary_ids | character | NULL | Filter to specific vocabularies |
max_levels | integer | 10 | Maximum hierarchy levels (max 20) |
relationship_types | character | NULL | Relationship types to follow (default: “Is a”) |
include_distance | logical | TRUE | Include hierarchy_level field |
include_paths | logical | FALSE | Include path information |
include_invalid | logical | TRUE | Include deprecated/invalid concepts |
domain_ids | character | NULL | Filter by domains |
page | integer | 1 | Page number |
page_size | integer | 100 | Results per page |
Get Relationship Types
Get available relationship types from the OMOP CDM:
# Get relationship types with pagination
result <- client$relationships$types(page = 1, page_size = 100)
for (rel_type in result$data) {
cat(sprintf("%s: %s\n", rel_type$relationship_id, rel_type$relationship_name))
}
# Access pagination
cat(sprintf("Total types: %d\n", result$meta$pagination$total_items))
With Options
Include synonyms, relationships, hierarchy, and specify vocabulary release:
# Get concept with synonyms
concept <- client$concepts$get(
201826,
include_synonyms = TRUE
)
# Get concept with synonyms and relationships
concept <- client$concepts$get(
201826,
include_synonyms = TRUE,
include_relationships = TRUE
)
print(concept$relationships) # list(parents = [...], children = [...])
# Get concept with hierarchy information
concept <- client$concepts$get(
201826,
include_hierarchy = TRUE
)
print(concept$hierarchy) # Ancestor/descendant summary
# Specify vocabulary release version
concept <- client$concepts$get(
201826,
vocab_release = "2025.2"
)
Parameters
| Parameter | Type | Default | Description |
|---|
concept_id | integer | required | The OMOP concept ID |
include_relationships | logical | FALSE | Include related concepts (parents/children) |
include_synonyms | logical | FALSE | Include concept synonyms |
include_hierarchy | logical | FALSE | Include hierarchy information |
vocab_release | character | NULL | Specific vocabulary release (e.g., “2025.2”) |
Get Concept Relationships
Get detailed relationships for a concept with filtering options:
# Get all relationships
result <- client$concepts$relationships(201826)
for (rel in result$data$relationships) {
cat(sprintf("%s: %s\n", rel$relationship_id, rel$concept_2$concept_name))
}
# Filter by relationship type and vocabulary
result <- client$concepts$relationships(
201826,
relationship_ids = c("Is a", "Subsumes"),
vocabulary_ids = "SNOMED",
standard_only = TRUE
)
# Include reverse relationships
result <- client$concepts$relationships(
201826,
include_reverse = TRUE,
domain_ids = c("Condition")
)
Relationships Parameters
| Parameter | Type | Default | Description |
|---|
concept_id | integer | required | The concept ID |
relationship_ids | character | NULL | Filter by relationship type IDs |
vocabulary_ids | character | NULL | Filter by target vocabulary IDs |
domain_ids | character | NULL | Filter by target domain IDs |
include_invalid | logical | TRUE | Include relationships to invalid concepts |
standard_only | logical | FALSE | Only include relationships to standard concepts |
include_reverse | logical | FALSE | Include reverse relationships |
vocab_release | character | NULL | Specific vocabulary release version |
# Basic related concepts
result <- client$concepts$related(201826, page_size = 10)
for (related in result$data) {
cat(sprintf("%s (%s): score %.2f\n",
related$concept_name,
related$relationship_id,
related$relationship_score
))
}
# Filter by relationship type and minimum score
result <- client$concepts$related(
201826,
relationship_types = c("Is a", "Maps to"),
min_score = 0.5,
page_size = 20
)
# Specify vocabulary release
result <- client$concepts$related(
201826,
vocab_release = "2025.1"
)
Get Recommended Concepts
Get curated concept recommendations using the OHDSI Phoebe algorithm:
# Basic recommendations for diabetes-related concepts
result <- client$concepts$recommended(c(201826, 4329847))
for (source_id in names(result$data)) {
cat(sprintf("\nRecommendations for concept %s:\n", source_id))
for (rec in head(result$data[[source_id]], 5)) {
cat(sprintf(" - %s (%s) via %s\n",
rec$concept_name,
rec$vocabulary_id,
rec$relationship_id
))
}
}
# With filters
result <- client$concepts$recommended(
c(201826),
relationship_types = c("Has finding", "Associated finding"),
vocabulary_ids = c("SNOMED", "LOINC"),
domain_ids = c("Condition", "Measurement"),
standard_only = TRUE,
page_size = 50
)
# Access pagination metadata
cat(sprintf("Page %d of %d\n",
result$meta$pagination$page,
result$meta$pagination$total_pages
))
cat(sprintf("Total recommendations: %d\n", result$meta$pagination$total_items))
