pubmed_search: Search PubMed for articles with optimized performance

In LBDiscover: Literature-Based Discovery Tools for Biomedical Research

Search PubMed for articles with optimized performance

Description

This function searches PubMed using the NCBI E-utilities API via the rentrez package. The implementation includes optimizations for speed, memory efficiency, and reliability.

Usage

pubmed_search(
  query,
  max_results = 1000,
  use_mesh = FALSE,
  date_range = NULL,
  api_key = NULL,
  batch_size = 200,
  verbose = TRUE,
  use_cache = TRUE,
  retry_count = 3,
  retry_delay = 1
)

Arguments

query	Character string containing the search query.
max_results	Maximum number of results to return.
use_mesh	Logical. If TRUE, will attempt to map query terms to MeSH terms.
date_range	Character vector of length 2 with start and end dates in format "YYYY/MM/DD".
api_key	Character string. NCBI API key for higher rate limits (optional).
batch_size	Integer. Number of records to fetch in each batch (default: 200).
verbose	Logical. If TRUE, prints progress information.
use_cache	Logical. If TRUE, cache results to avoid redundant API calls.
retry_count	Integer. Number of times to retry failed API calls.
retry_delay	Integer. Initial delay between retries in seconds.

Value

A data frame containing the search results with PubMed IDs, titles, and other metadata.

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