map_ontology: Map terms to biomedical ontologies

In LBDiscover: Literature-Based Discovery Tools for Biomedical Research

Map terms to biomedical ontologies

Description

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

LBDiscover documentation built on June 16, 2025, 5:09 p.m.