easyPubMed (version 3.1.6)

EPM_esearch_efetch_seq: Retrieve Results via an Esearch and Efetch sequence.

Description

Submit a Query to the NCBI ESearch Server, capture the response and retrieve the corresponding PubMed records from the NCBI EFetch Server. Up to the first n=10,000 records returned by the query will be retrieved (as per the NCBI policy). This does not include a timeout limit to complete the operation.

Usage

EPM_esearch_efetch_seq(
  query_string,
  api_key = NULL,
  batch_size = 500,
  encoding = "UTF-8",
  format = "xml",
  max_restart_attempts = 10
)

Value

Character vector including the response from the server.

Arguments

query_string

String (character vector of length 1), corresponding to the query URL to the remote server.

api_key

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

batch_size

Integer, max number of records to be retrieved as a batch. This corresponds to the "retmax" NCBI parameter.

encoding

String (character vector of length 1), encoding of the resulting records (e.g., "UTF-8").

format

String (character vector of length 1), desired format of the Pubmed records. This must be one of the values in c("xml", "medline", "uilist").

max_restart_attempts

Integer, max number of attempts in case of a failed iteration.

Author

Damiano Fantini,

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]'
  easyPubMed:::EPM_esearch_efetch_seq(query_string = qry, format = "uilist")
}, silent = TRUE)
setTimeLimit(elapsed = Inf)