Search Europe PMC for publications — epmc

This function queries the Europe PMC REST API using a provided search string. It handles pagination using a cursor and returns a tibble of search results.

Usage

epmc_search(query, page_limit = 10, delay = 1)

Arguments

query: A character string representing the search query for Europe PMC. See https://europepmc.org/Help for query syntax.
page_limit: An integer specifying the maximum number of pages to retrieve. Defaults to 10. Set to Inf to retrieve all pages (use with caution).
delay: An integer delay for API calls. Defaults to 1.

Value

A tibble where each row represents a publication. Columns include:

id: Publication ID
source: Source of the publication (e.g., "MED", "PMC")
pmid: PubMed ID
pmcid: PubMed Central ID
doi: Digital Object Identifier
title: Title of the publication
authorString: String of authors
journalTitle: Title of the journal
issue: Journal issue
journalVolume: Journal volume
pubYear: Year of publication
journalIssn: Journal ISSN
pageInfo: Page information
pubType: Type of publication (e.g., "journal article", "review")
isOpenAccess: Whether the publication is open access ("OA" or "N/A")
inEPMC: Whether the publication is in EPMC ("Y" or "N/A")
inPMC: Whether the publication is in PMC ("Y" or "N/A")
hasPDF: Whether a PDF is available ("Y" or "N/A")
hasBook: Whether it is a book ("Y" or "N/A")
citedByCount: Number of citations
hasReferences: Whether references are available ("Y" or "N/A")
hasTextMinedTerms: Whether text-mined terms are available ("Y" or "N/A")
hasDbCrossReferences: Whether database cross-references are available ("Y" or "N/A")
hasLabsLinks: Whether Labs links are available ("Y" or "N/A")
hasTMAccessionNumbers: Whether TM accession numbers are available ("Y" or "N/A")
firstPublicationDate: Date of first publication

Examples

if (FALSE) { # \dontrun{
  # Search for publications related to "crispr"
  crispr_results <- epmc_search(query = "crispr")
  dplyr::glimpse(crispr_results)

  # Search for publications by a specific author
  author_results <- epmc_search(query = "AUTH:\"Smith J\"")
  dplyr::glimpse(author_results)
} # }