LBDiscover (version 0.1.0)

load_dictionary: 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
)

Value

A data frame containing the dictionary.

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).