Search for OMOP concepts by name

Searches the vocabulary tables across all connected DataSHIELD servers for concepts matching the given pattern and/or filters. Results include concept ID, name, domain, vocabulary, and standard concept flag. The search is executed server-side via omopSearchConceptsDS so that vocabulary tables never leave the server. Vocabulary metadata carries no patient data, so this reader is not disclosure-gated.

Usage

ds.omop.concept.search(
  pattern = NULL,
  domain = NULL,
  vocabulary = NULL,
  standard_only = TRUE,
  limit = 50,
  concept_id = NULL,
  standard = NULL,
  valid = NULL,
  symbol = "omop",
  conns = NULL,
  execute = TRUE
)

Arguments

pattern

Character; search term or SQL LIKE pattern to match against concept names. Supports partial matching (e.g., "diabetes" matches "Type 2 diabetes mellitus"). Now optional: pass NULL to search by concept_id or by the metadata filters alone.

domain

Character; restrict results to a specific OMOP domain (e.g., "Condition", "Drug", "Measurement"). NULL (the default) returns concepts from all domains.

vocabulary

Character; restrict results to a specific vocabulary (e.g., "SNOMED", "ICD10CM", "RxNorm"). NULL (the default) searches across all vocabularies.

standard_only

Logical; if TRUE (the default), only standard concepts are returned. Set to FALSE to include non-standard and classification concepts. Ignored when standard is supplied.

limit

Integer; maximum number of results to return per server (default: 50). Increase for broader searches, but larger values will increase server-side processing time.

concept_id

Integer or numeric vector; restrict the search to these exact concept IDs. NULL (the default) applies no ID filter.

standard

Character; explicit standard_concept value to filter on (e.g. "S" for standard, "C" for classification). When supplied this overrides standard_only. NULL (the default) applies no explicit value filter.

valid

Logical; TRUE keeps only currently-valid concepts (invalid_reason IS NULL), FALSE only invalidated ones. NULL (the default) returns both.

symbol

Character; the session symbol used when the OMOP connection was initialised (default: "omop").

conns

DSI connection object(s). If NULL (the default), the connections stored in the active session are used.

execute

Logical; if FALSE, returns a dry-run dsomop_result containing only the reproducible R code without contacting the servers.

Value

A dsomop_result object with scope = "pooled" (a de-duplicated cross-site view of the shared vocabulary; per-site frames remain available). Each server's result is a data frame with columns such as concept_id, concept_name, domain_id, vocabulary_id, and standard_concept.

Examples

if (FALSE) { # \dontrun{
# Search for diabetes-related conditions
results <- ds.omop.concept.search("diabetes", domain = "Condition")
results$pooled

# Search across all domains, including non-standard concepts
all_hits <- ds.omop.concept.search("aspirin", standard_only = FALSE, limit = 100)

# Look up exact IDs, keeping only currently-valid standard concepts
hits <- ds.omop.concept.search(NULL, concept_id = c(201826, 4329847),
                               standard = "S", valid = TRUE)
} # }