Convert PubMed IDs (PMIDs) to PMC IDs

Source: R/pmid_to_pmc.R

This function converts a vector of PubMed IDs (PMIDs) to their corresponding PubMed Central (PMC) IDs and DOIs using the NCBI ID Converter API.

pmid_to_pmc(pmids, batch_size = 200L, sleep = 0.5)

Arguments

pmids

A character or numeric vector of PubMed IDs (PMIDs) to convert.

batch_size

An integer specifying the number of PMIDs to process per batch. Defaults to 200L. The NCBI API has limitations on batch sizes.

sleep

A numeric value specifying the number of seconds to pause between API requests. Defaults to 0.5 seconds to respect API rate limits.

Value

A data.table with columns:

  • pmid: The input PubMed ID

  • pmcid: The corresponding PMC ID (NA if not available in PMC)

  • doi: The corresponding DOI (NA if not available)

Results are ordered by PMID. Returns NULL with a message if the API is unavailable or returns invalid data.

Examples

# \donttest{
if (interactive()) {
  # Convert a single PMID to PMC ID
  result <- pmid_to_pmc("12345678")
  
  # Convert multiple PMIDs
  pmids <- c("12345678", "23456789", "34567890")
  result <- pmid_to_pmc(pmids, batch_size = 10, sleep = 1)
}
# }