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

Source: R/get_records.R

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_references",
    "pubmed_abstracts", "pmc_fulltext"),
  cores = 3,
  sleep = 1,
  ncbi_key = NULL
)

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_references', '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.

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)