EPM_efetch_basic_q: Submit a Query to the NCBI EFetch Server.

In dami82/easyPubMed: Search and Retrieve Scientific Publication Records from PubMed

Submit a Query to the NCBI EFetch Server.

Description

Submit a Query to the NCBI EFetch Server and capture the response.

Usage

EPM_efetch_basic_q(params)

Arguments

params

List including the information for querying the NCBI EFetch Server.

Details

The input list must include the elements listed below.

• 'web_env'. String, unique value returned by the NCBI ESearch server.

• 'format'. String corresponding to the desired response data format (e.g., "xml").

• 'query_key'. Integer, key value returned by the NCBI ESearch server.

• 'retstart'. Integer, numeric index of the first record to be request.

• 'retmax'. Integer, maximum number of records to be retrieved from the server.

• 'encoding'. String, encoding of the data (e.g., "UTF-8").

Value

Character vector including the response from the server.

Author(s)

Damiano Fantini, [e-mail]

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({
  x <- easyPubMed:::EPM_esearch_basic_q(params = list(q = "easyPubMed"))
  x <- easyPubMed:::EPM_esearch_parse(x)
  my_params <- list(web_env = x$web_env, 
                    query_key = x$query_key, 
                    format = "uilist")
  easyPubMed:::EPM_efetch_basic_q(params = my_params)
}, silent = TRUE)
setTimeLimit(elapsed = Inf)

dami82/easyPubMed documentation built on Jan. 4, 2024, 6:21 a.m.