Retrieve Data from 'NLM'/'PubMed' databases Based on PMIDs

This function retrieves different types of data (like 'PubMed' records, affiliations, 'iCites 'data, etc.) from 'PubMed' based on provided PMIDs. It supports parallel processing for efficiency.

get_records(
  pmids,
  endpoint = c("pubtations", "icites", "pubmed_affiliations", "pubmed_abstracts",
    "pmc_fulltext"),
  cores = 3,
  sleep = 1,
  ncbi_key = NULL,
  icite_timeout = getOption("puremoe.icite_timeout", 15)
)

Arguments

pmids: A vector of PMIDs for which data is to be retrieved. For 'pmc_fulltext' endpoint, provide full URLs instead (e.g., from pmid_to_pmc()$url).
endpoint: A character vector specifying the type of data to retrieve ('pubtations', 'icites', 'pubmed_affiliations', 'pubmed_abstracts', 'pmc_fulltext').
cores: Number of cores to use for parallel processing (default is 3).
sleep: Duration (in seconds) to pause after each batch
ncbi_key: (Optional) NCBI API key for authenticated access.
icite_timeout: Maximum elapsed seconds to allow each iCite batch before skipping it and returning PMID-only rows. Defaults to the puremoe.icite_timeout option, or 15 seconds if unset.

Value

A data.table containing combined results from the specified endpoint.

Details

For the 'pmc_fulltext' endpoint, provide full URLs to PMC tar.gz files. Use pmid_to_pmc to convert PMIDs to PMC IDs and full URLs first.

Examples

pmids <- c("38136652")
results <- get_records(pmids, endpoint = "pubmed_abstracts", cores = 1)