load_dictionary: Load biomedical dictionaries with improved error handling

In LBDiscover: Literature-Based Discovery Tools for Biomedical Research

Load biomedical dictionaries with improved error handling

Description

This function loads pre-defined biomedical dictionaries or fetches terms from MeSH/UMLS.

Usage

load_dictionary(
  dictionary_type = NULL,
  custom_path = NULL,
  source = c("local", "mesh", "umls"),
  api_key = NULL,
  n_terms = 200,
  mesh_query = NULL,
  semantic_type_filter = NULL,
  sanitize = TRUE,
  extended_mesh = FALSE,
  mesh_queries = NULL
)

Arguments

dictionary_type	Type of dictionary to load. For local dictionaries, limited to "disease", "drug", "gene". For MeSH and UMLS, expanded to include more semantic categories.
custom_path	Optional path to a custom dictionary file.
source	The source to fetch terms from: "local", "mesh", or "umls".
api_key	UMLS API key for authentication (required if source = "umls").
n_terms	Number of terms to fetch.
mesh_query	Additional query to filter MeSH terms (only if source = "mesh").
semantic_type_filter	Filter by semantic type (used mainly with UMLS).
sanitize	Logical. If TRUE, sanitizes the dictionary terms.
extended_mesh	Logical. If TRUE and source is "mesh", uses PubMed search for additional terms.
mesh_queries	Named list of MeSH queries for different categories (only if extended_mesh = TRUE).

Value

A data frame containing the dictionary.

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