Map terms to biomedical ontologies — map

This function maps terms to standard biomedical ontologies like MeSH or UMLS.

Usage

map_ontology(
  terms,
  ontology = c("mesh", "umls"),
  api_key = NULL,
  fuzzy_match = FALSE,
  similarity_threshold = 0.8,
  mesh_query = NULL,
  semantic_types = NULL,
  dictionary_type = "disease"
)

Arguments

terms: Character vector of terms to map
ontology: Character string. The ontology to use: "mesh" or "umls"
api_key: UMLS API key (required if ontology = "umls")
fuzzy_match: Logical. If TRUE, allows fuzzy matching of terms
similarity_threshold: Numeric between 0 and 1. Minimum similarity for fuzzy matching
mesh_query: Additional query to filter MeSH terms (only if ontology = "mesh")
semantic_types: Vector of semantic types to filter UMLS results
dictionary_type: Type of dictionary to use ("disease", "drug", "gene", etc.)

Value

A data frame with mapped terms and ontology identifiers

Examples

if (FALSE) { # \dontrun{
# Map terms to MeSH
mesh_mappings <- map_ontology(c("headache", "migraine"), ontology = "mesh")

# Map terms to UMLS with API key
umls_mappings <- map_ontology(c("headache", "migraine"), ontology = "umls",
                              api_key = "your_api_key")
} # }