RefManageR (version 1.4.0)

GetPubMedRelated: Retrieve related articles from PubMed using PubMed ID's

Description

Searches PubMed for articles related to a set of PubMed ID's using NCBI's E-Utilities.

Usage

GetPubMedRelated(
  id,
  database = "pubmed",
  batch.mode = TRUE,
  max.results = 10,
  return.sim.scores = FALSE,
  return.related.ids = FALSE
)

Value

an object of class BibEntry.

Arguments

id

either a character vector of PubMed ID's or a BibEntry object, which is expected to have at least some entries with eprinttype = "pubmed" and eprint field specifying a PubMed ID.

database

string; the Entrez database to search

batch.mode

logical; if TRUE, the PubMed IDs in id are combined by Entrez when searching for linked IDs so that only one set of linked IDs is returned. If FALSE, a set of linked IDs is obtained for each ID in id. will be returned

max.results

numeric vector; the maximum number of results to return if batch.mode TRUE; or if batch.mode is FALSE, this should have the same length as id with each element giving the maximum number of results to return for the corresponding ID.

return.sim.scores

logical; Entrez returns a similarity score with each returned citation giving a measure of how similar the returned entry is to the ones specified by the query. If TRUE these scores are added to the returned BibEntry object in a field called ‘score’.

return.related.ids

logical; should the original PubMed ID(s) that a returned entry is related to be stored in a field called ‘PMIDrelated’.

References

https://www.ncbi.nlm.nih.gov/books/NBK25500/

See Also

Other pubmed: GetPubMedByID(), LookupPubMedID(), 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)
  bib <- LookupPubMedID(bib[[101:102]])
  toBiblatex(GetPubMedRelated(bib, batch.mode = TRUE, max.results = 2,
  return.sim.scores = TRUE, return.related.ids = TRUE))
  GetPubMedRelated(bib, batch.mode = FALSE, max.results = c(2, 2))
}