run_lbd: Perform comprehensive literature-based discovery without type...

In LBDiscover: Literature-Based Discovery Tools for Biomedical Research

Perform comprehensive literature-based discovery without type constraints

Description

This function performs a comprehensive literature-based discovery analysis using multiple approaches without enforcing entity type constraints.

Usage

run_lbd(
  search_query,
  a_term,
  max_results = 100,
  discovery_approaches = c("abc", "anc", "lsi", "bitola"),
  include_visualizations = TRUE,
  output_file,
  api_key = NULL,
  dictionary_sources = c("local", "mesh", "umls"),
  entity_categories = c("disease", "drug", "gene")
)

Arguments

search_query	Character string, the search query for retrieving initial articles.
a_term	Character string, the source term (A) for discovery.
max_results	Maximum number of results to return for each approach.
discovery_approaches	Character vector, the discovery approaches to use.
include_visualizations	Logical. If TRUE, generates visualizations.
output_file	File path for the output report. Must be specified by user.
api_key	Character string. API key for PubMed and other services.
dictionary_sources	Character vector. Sources for entity dictionaries: "local", "mesh", "umls".
entity_categories	Character vector. Entity categories to include.

Value

A list containing discovery results from all approaches.

Examples

# Example with temporary output file
temp_report <- file.path(tempdir(), "discovery_report.html")

results <- run_lbd(
  search_query = "migraine treatment",
  a_term = "migraine",
  max_results = 10,
  discovery_approaches = "abc",
  include_visualizations = FALSE,
  output_file = temp_report
)

# Clean up
unlink(temp_report)
unlink(list.files(tempdir(), pattern = "*.png", full.names = TRUE))
unlink(list.files(tempdir(), pattern = "*.html", full.names = TRUE))

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