easyPubMed (version 3.1.6)

get_pubmed_ids: Simple PubMed Record Search

Description

Query PubMed (Entrez) in a simple way via the PubMed API eSearch function. Calling this function results in posting the query results on the PubMed History Server. This allows later access to the resulting data via the fetch_pubmed_data() function, or other easyPubMed functions. NOTE: this function has become obsolete. You should use the epm_query() function instead. Please, have a look at the manual or the vignette. The get_pubmed_ids() function will be retired in 2026.

Usage

get_pubmed_ids(pubmed_query_string, api_key = NULL)

Value

An easyPubMed object which includes no PubMed records.

Arguments

pubmed_query_string

String (character vector of length 1), corresponding to the query string used for querying PubMed.

api_key

String (character vector of length 1), corresponding to the NCBI API key. Can be NULL.

Author

Damiano Fantini,

Details

This function will use the String provided as argument for querying PubMed via the eSearch function of the PubMed API. The Query Term can include one or multiple words, as well as the standard PubMed operators (AND, OR, NOT) and tags (i.e., [AU], [PDAT], [Affiliation], and so on). ESearch will post the UIDs resulting from the search operation onto the History server so that they can be used directly in a subsequent fetchPubmedData() call.

References

https://www.data-pulse.com/dev_site/easypubmed/

Examples

# Note: a time limit can be set in order to kill the operation when/if 
# the NCBI/Entrez server becomes unresponsive.
setTimeLimit(elapsed = 4.9)
try({
  qry <- 'Damiano Fantini[AU] AND "2018"[PDAT]'
  get_pubmed_ids(pubmed_query_string = qry)
}, silent = TRUE)
setTimeLimit(elapsed = Inf)