puremoe (version 1.0.3)

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

Description

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.

Usage

get_records(
  pmids,
  endpoint = c("pubtations", "icites", "pubmed_affiliations", "pubmed_references",
    "pubmed_abstracts", "pmc_fulltext"),
  cores = 3,
  sleep = 1,
  ncbi_key = NULL
)

Value

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

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.

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)