pmFetchById: Fetch PubMed records by PMID

Description

It downloads metadata for a set of PubMed articles identified by their PMID (PubMed Identifier). This is useful for retrieving specific known articles, updating existing datasets, or downloading records identified through other sources.

Usage

pmFetchById(pmids, api_key = NULL, batch_size = 200)

Value

a list following the same structure as pmApiRequest output, containing:

data		The xml-structured list containing the bibliographic metadata.
query		A character string describing the PMID-based query.
query_translation		Same as query for PMID-based searches.
records_downloaded		The total number of records downloaded.
total_count		The total number of PMIDs requested.

Arguments

pmids: is a character or numeric vector. A vector of PubMed identifiers (PMIDs).
api_key: is a character. It contains a valid API key for the NCBI E-utilities. Default is api_key=NULL. The API key can also be set via the environment variable PUBMED_API_KEY or ENTREZ_KEY.
batch_size: is numeric. The number of records to download per API request. Default is 200.

Details

The function uses the NCBI E-utilities efetch endpoint to retrieve records directly by their PMIDs, without requiring a search query. Records are downloaded in batches to respect API rate limits.

The output is compatible with pmApi2df for conversion to a dataframe.

Examples

Run this code


# \donttest{
# Download specific articles by PMID
pmids <- c("34813985", "34813456", "34812345")
D <- pmFetchById(pmids = pmids)
M <- pmApi2df(D)
# }