SearchResource: Search Resource
In omophub: R Client for the 'OMOPHub' Medical Vocabulary API
SearchResource R Documentation
Search Resource
Description
R6 class providing access to search operations.
Value
Search results with pagination.
A tibble of all matching concepts.
Search results with facets and metadata.
Autocomplete suggestions.
List with results and pagination metadata.
A tibble of all matching concepts with similarity scores.
List with similar_concepts and search_metadata.
Methods
Public methods
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Method new()
Create a new SearchResource.
Usage
SearchResource$new(base_req)
Arguments
base_reqBase httr2 request object.
Method basic()
Basic concept search.
Usage
SearchResource$basic(
query,
vocabulary_ids = NULL,
domain_ids = NULL,
concept_class_ids = NULL,
standard_concept = NULL,
include_synonyms = FALSE,
include_invalid = FALSE,
min_score = NULL,
exact_match = FALSE,
page = 1,
page_size = 20,
sort_by = NULL,
sort_order = NULL
)
Arguments
querySearch query string.
vocabulary_idsFilter by vocabulary IDs.
domain_idsFilter by domain IDs.
concept_class_idsFilter by concept class IDs.
standard_conceptFilter by standard concept ("S", "C", or NULL).
include_synonymsSearch in synonyms. Default FALSE.
include_invalidInclude invalid concepts. Default FALSE.
min_scoreMinimum relevance score.
exact_matchRequire exact match. Default FALSE.
pagePage number (1-based). Default 1.
page_sizeResults per page. Default 20.
sort_bySort field.
sort_orderSort order ("asc" or "desc").
Method basic_all()
Fetch all search results with automatic pagination.
Usage
SearchResource$basic_all(
query,
vocabulary_ids = NULL,
domain_ids = NULL,
page_size = 100,
max_pages = Inf,
progress = TRUE,
...
)
Arguments
querySearch query string.
vocabulary_idsFilter by vocabulary IDs.
domain_idsFilter by domain IDs.
page_sizeResults per page. Default 100.
max_pagesMaximum pages to fetch. Default Inf.
progressShow progress bar. Default TRUE.
...Additional search parameters.
Method advanced()
Advanced concept search with facets.
Usage
SearchResource$advanced(
query,
vocabulary_ids = NULL,
domain_ids = NULL,
concept_class_ids = NULL,
standard_concepts_only = FALSE,
include_invalid = FALSE,
relationship_filters = NULL,
page = 1,
page_size = 20
)
Arguments
querySearch query string.
vocabulary_idsFilter by vocabulary IDs.
domain_idsFilter by domain IDs.
concept_class_idsFilter by concept class IDs.
standard_concepts_onlyOnly return standard concepts. Default FALSE.
include_invalidInclude invalid concepts. Default FALSE.
relationship_filtersRelationship-based filters.
pagePage number (1-based). Default 1.
page_sizeResults per page. Default 20.
Method autocomplete()
Get autocomplete suggestions.
Usage
SearchResource$autocomplete(
query,
vocabulary_ids = NULL,
domains = NULL,
max_suggestions = 10
)
Arguments
queryPartial query string.
vocabulary_idsFilter by vocabulary IDs.
domainsFilter by domains.
max_suggestionsMaximum suggestions. Default 10.
Method semantic()
Semantic concept search using neural embeddings.
Usage
SearchResource$semantic(
query,
vocabulary_ids = NULL,
domain_ids = NULL,
standard_concept = NULL,
concept_class_id = NULL,
threshold = NULL,
page = 1,
page_size = 20
)
Arguments
queryNatural language search query (required).
vocabulary_idsFilter by vocabulary IDs.
domain_idsFilter by domain IDs.
standard_conceptFilter by standard concept ('S' or 'C').
concept_class_idFilter by concept class ID.
thresholdMinimum similarity threshold (0.0-1.0, default 0.5).
pagePage number (1-based). Default 1.
page_sizeResults per page (max 100). Default 20.
Method semantic_all()
Fetch all semantic search results with automatic pagination.
Usage
SearchResource$semantic_all(
query,
vocabulary_ids = NULL,
domain_ids = NULL,
standard_concept = NULL,
concept_class_id = NULL,
threshold = NULL,
page_size = 100,
max_pages = Inf,
progress = TRUE
)
Arguments
queryNatural language search query (required).
vocabulary_idsFilter by vocabulary IDs.
domain_idsFilter by domain IDs.
standard_conceptFilter by standard concept ('S' or 'C').
concept_class_idFilter by concept class ID.
thresholdMinimum similarity threshold (0.0-1.0).
page_sizeResults per page. Default 100.
max_pagesMaximum pages to fetch. Default Inf.
progressShow progress bar. Default TRUE.
Method similar()
Find concepts similar to a reference concept or query.
Must provide exactly one of: concept_id, concept_name, or query.
Usage
SearchResource$similar(
concept_id = NULL,
concept_name = NULL,
query = NULL,
algorithm = "hybrid",
similarity_threshold = 0.7,
page_size = 20,
vocabulary_ids = NULL,
domain_ids = NULL,
standard_concept = NULL,
include_invalid = NULL,
include_scores = NULL,
include_explanations = NULL
)
Arguments
concept_idConcept ID to find similar concepts for.
concept_nameConcept name to find similar concepts for.
queryNatural language query for semantic similarity.
algorithmOne of 'semantic', 'lexical', or 'hybrid' (default).
similarity_thresholdMinimum similarity (0.0-1.0). Default 0.7.
page_sizeMax results (max 1000). Default 20.
vocabulary_idsFilter by vocabulary IDs.
domain_idsFilter by domain IDs.
standard_conceptFilter by standard concept flag ('S', 'C', or 'N').
include_invalidInclude invalid/deprecated concepts.
include_scoresInclude detailed similarity scores.
include_explanationsInclude similarity explanations.
Method print()
Print resource information.
Usage
SearchResource$print()
Method clone()
The objects of this class are cloneable with this method.
Usage
SearchResource$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
Note
When algorithm='semantic', only single vocabulary/domain filter supported.
omophub documentation built on Feb. 23, 2026, 5:09 p.m.
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| SearchResource | R Documentation |
Search Resource
Description
R6 class providing access to search operations.
Value
Search results with pagination.
A tibble of all matching concepts.
Search results with facets and metadata.
Autocomplete suggestions.
List with results and pagination metadata.
A tibble of all matching concepts with similarity scores.
List with similar_concepts and search_metadata.
Methods
Public methods
Method new()
Create a new SearchResource.
Usage
SearchResource$new(base_req)
Arguments
base_reqBase httr2 request object.
Method basic()
Basic concept search.
Usage
SearchResource$basic( query, vocabulary_ids = NULL, domain_ids = NULL, concept_class_ids = NULL, standard_concept = NULL, include_synonyms = FALSE, include_invalid = FALSE, min_score = NULL, exact_match = FALSE, page = 1, page_size = 20, sort_by = NULL, sort_order = NULL )
Arguments
querySearch query string.
vocabulary_idsFilter by vocabulary IDs.
domain_idsFilter by domain IDs.
concept_class_idsFilter by concept class IDs.
standard_conceptFilter by standard concept ("S", "C", or NULL).
include_synonymsSearch in synonyms. Default
FALSE.include_invalidInclude invalid concepts. Default
FALSE.min_scoreMinimum relevance score.
exact_matchRequire exact match. Default
FALSE.pagePage number (1-based). Default 1.
page_sizeResults per page. Default 20.
sort_bySort field.
sort_orderSort order ("asc" or "desc").
Method basic_all()
Fetch all search results with automatic pagination.
Usage
SearchResource$basic_all( query, vocabulary_ids = NULL, domain_ids = NULL, page_size = 100, max_pages = Inf, progress = TRUE, ... )
Arguments
querySearch query string.
vocabulary_idsFilter by vocabulary IDs.
domain_idsFilter by domain IDs.
page_sizeResults per page. Default 100.
max_pagesMaximum pages to fetch. Default Inf.
progressShow progress bar. Default
TRUE....Additional search parameters.
Method advanced()
Advanced concept search with facets.
Usage
SearchResource$advanced( query, vocabulary_ids = NULL, domain_ids = NULL, concept_class_ids = NULL, standard_concepts_only = FALSE, include_invalid = FALSE, relationship_filters = NULL, page = 1, page_size = 20 )
Arguments
querySearch query string.
vocabulary_idsFilter by vocabulary IDs.
domain_idsFilter by domain IDs.
concept_class_idsFilter by concept class IDs.
standard_concepts_onlyOnly return standard concepts. Default
FALSE.include_invalidInclude invalid concepts. Default
FALSE.relationship_filtersRelationship-based filters.
pagePage number (1-based). Default 1.
page_sizeResults per page. Default 20.
Method autocomplete()
Get autocomplete suggestions.
Usage
SearchResource$autocomplete( query, vocabulary_ids = NULL, domains = NULL, max_suggestions = 10 )
Arguments
queryPartial query string.
vocabulary_idsFilter by vocabulary IDs.
domainsFilter by domains.
max_suggestionsMaximum suggestions. Default 10.
Method semantic()
Semantic concept search using neural embeddings.
Usage
SearchResource$semantic( query, vocabulary_ids = NULL, domain_ids = NULL, standard_concept = NULL, concept_class_id = NULL, threshold = NULL, page = 1, page_size = 20 )
Arguments
queryNatural language search query (required).
vocabulary_idsFilter by vocabulary IDs.
domain_idsFilter by domain IDs.
standard_conceptFilter by standard concept ('S' or 'C').
concept_class_idFilter by concept class ID.
thresholdMinimum similarity threshold (0.0-1.0, default 0.5).
pagePage number (1-based). Default 1.
page_sizeResults per page (max 100). Default 20.
Method semantic_all()
Fetch all semantic search results with automatic pagination.
Usage
SearchResource$semantic_all( query, vocabulary_ids = NULL, domain_ids = NULL, standard_concept = NULL, concept_class_id = NULL, threshold = NULL, page_size = 100, max_pages = Inf, progress = TRUE )
Arguments
queryNatural language search query (required).
vocabulary_idsFilter by vocabulary IDs.
domain_idsFilter by domain IDs.
standard_conceptFilter by standard concept ('S' or 'C').
concept_class_idFilter by concept class ID.
thresholdMinimum similarity threshold (0.0-1.0).
page_sizeResults per page. Default 100.
max_pagesMaximum pages to fetch. Default Inf.
progressShow progress bar. Default
TRUE.
Method similar()
Find concepts similar to a reference concept or query.
Must provide exactly one of: concept_id, concept_name, or query.
Usage
SearchResource$similar( concept_id = NULL, concept_name = NULL, query = NULL, algorithm = "hybrid", similarity_threshold = 0.7, page_size = 20, vocabulary_ids = NULL, domain_ids = NULL, standard_concept = NULL, include_invalid = NULL, include_scores = NULL, include_explanations = NULL )
Arguments
concept_idConcept ID to find similar concepts for.
concept_nameConcept name to find similar concepts for.
queryNatural language query for semantic similarity.
algorithmOne of 'semantic', 'lexical', or 'hybrid' (default).
similarity_thresholdMinimum similarity (0.0-1.0). Default 0.7.
page_sizeMax results (max 1000). Default 20.
vocabulary_idsFilter by vocabulary IDs.
domain_idsFilter by domain IDs.
standard_conceptFilter by standard concept flag ('S', 'C', or 'N').
include_invalidInclude invalid/deprecated concepts.
include_scoresInclude detailed similarity scores.
include_explanationsInclude similarity explanations.
Method print()
Print resource information.
Usage
SearchResource$print()
Method clone()
The objects of this class are cloneable with this method.
Usage
SearchResource$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
Note
When algorithm='semantic', only single vocabulary/domain filter supported.
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