Fetch works from PubMed — sm_fetch_pubmed • scimapR

Query PubMed via the NCBI E-utilities (esearch + efetch) and return the results as an sm_corpus.

Uses retmax/retstart pagination to retrieve up to n_max records. Providing an NCBI API key allows up to 10 requests/second instead of 3.

Usage

sm_fetch_pubmed(
  query,
  n_max = 200L,
  api_key = Sys.getenv("NCBI_API_KEY"),
  engine = c("native", "rentrez", "auto"),
  verbose = TRUE,
  call = rlang::caller_env()
)

Arguments

query: PubMed search query string (required).
n_max: Maximum number of records to return (default 200).
api_key: NCBI API key. Read from NCBI_API_KEY env var by default.
engine: One of "native" (built-in httr2 client), "rentrez" (use the rentrez package), or "auto" (use rentrez if available, otherwise native).
verbose: Print progress messages?
call: Caller environment for error reporting.

Value

An sm_corpus object.

See also

Other fetchers: sm_fetch_arxiv(), sm_fetch_biorxiv(), sm_fetch_crossref(), sm_fetch_openalex(), sm_fetch_orcid(), sm_fetch_overton(), sm_fetch_semantic_scholar()

Examples

if (FALSE) { # \dontrun{
corpus <- sm_fetch_pubmed(query = "bibliometrics[tiab]", n_max = 10)
print(corpus)
} # }