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Retrieve PubMed ID's for a BibEntry object

Source: R/ReadPubMed.R
LookupPubMedID.Rd

Uses the NCBI E-utilities to to search for PubMed ID's for citations stored in a BibEntry object.

Usage

LookupPubMedID(bib, index)

Arguments

bib

a bibentry object

index

indices specifying which entries of bib will be searched for. If missing, all entries are searched for.

Value

a BibEntry object - bib with additional eprinttype and eprint fields when the search is successful for an entry.

Details

For each entry a citation string is created using the fields journaltitle/journal, date/year, volume, pages, and author; and these strings are then used to search the NCBI database for PubMed ID's.

If an ID is found for an entry, the entry is updated so that the eprinttype field is assigned the value “pubmed” and the eprint field is assigned the ID.

See also

Other pubmed: GetPubMedByID(), GetPubMedRelated(), ReadCrossRef(), ReadPubMed()

Examples

if (interactive() && !httr::http_error("https://eutils.ncbi.nlm.nih.gov/")){
  file.name <- system.file("Bib", "RJC.bib", package = "RefManageR")
  bib <- ReadBib(file.name)
  LookupPubMedID(bib[[101:102]])
}