Skip to contents

Load biomedical dictionaries with improved error handling

Source: R/text_preprocessing.R
load_dictionary.Rd

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.

Examples

# Load a disease dictionary from local source
disease_dict <- load_dictionary("disease", source = "local")
#> Package not installed or dictionary not found. Using example dictionaries.
#> Creating dummy dictionary for disease
#> Sanitizing dictionary with 8 terms...
#>   Removed 6 terms that did not match their claimed entity types
#> Sanitization complete. 2 terms remaining (25% of original)
head(disease_dict)
#>       term        id    type source
#> 1 migraine DISEASE_1 disease  dummy
#> 6   cancer DISEASE_6 disease  dummy

# Load with custom terms
custom_dict <- data.frame(
  term = c("migraine", "headache", "photophobia"),
  type = c("disease", "symptom", "symptom"),
  id = c("D001", "D002", "D003"),
  source = rep("custom", 3)
)
print(custom_dict)
#>          term    type   id source
#> 1    migraine disease D001 custom
#> 2    headache symptom D002 custom
#> 3 photophobia symptom D003 custom