easyPubMed (version 3.1.6)

fetch_pubmed_data: Retrieve PubMed Data in XML or TXT Format

Description

Retrieve PubMed records from Entrez following a search performed via the get_pubmed_ids() function. Data are downloaded in the XML or TXT format and are retrieved in batches of up to 5000 records.

Usage

fetch_pubmed_data(
  pubmed_id_list,
  retstart = 0,
  retmax = 500,
  format = "xml",
  encoding = "UTF8",
  api_key = NULL,
  verbose = TRUE
)

Value

Character vector of length >= 1. If format is set to "xml" (default), a single String including all PubMed records (decorated with XML tags) is returned. If a different format is selected, a vector of strings is returned, where each element corresponds to a line of the output document.

Arguments

pubmed_id_list

An easyPubMed object.

retstart

Integer (>=0): this argument is ignored.

retmax

Integer (>=1): this argument is ignored.

format

String: element specifying the output format. The following values are allowed: c("xml", "medline", "uilist").

encoding

String, the encoding of the records retrieved from Pubmed. This argument is ignored and set to 'UTF-8'.

api_key

String, corresponding to the NCBI API token (if available). NCBI token strings can be requested from NCBI. Record download will be faster if a valid NCBI token is used. This argument can be NULL.

verbose

Logical, shall details about the progress of the operation be printed to console.

Author

Damiano Fantini

Details

The `fetch_pubmed_data()` function is now obsolete. You should use the `epm_fetch()` function instead. Please, have a look at the manual or the vignette. The `fetch_pubmed_data()` function will be retired in 2026.

References

https://www.data-pulse.com/dev_site/easypubmed/ https://www.ncbi.nlm.nih.gov/books/NBK25499/table/chapter4.T._valid_values_of__retmode_and/

Examples

## Example 01: retrieve PubMed record Unique Identifiers (uilist)
# 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({ 
  q <- 'Damiano Fantini[AU] AND "2018"[PDAT]'
  x <- get_pubmed_ids(pubmed_query_string = q)
  y <- fetch_pubmed_data(x, format = "uilist")
  y
}, silent = TRUE)
setTimeLimit(elapsed = Inf)

if (FALSE) {
## Example 02: retrieve data in XML format
q <- 'Damiano Fantini[AU] AND "2018"[PDAT]'
x <- epm_query(query_string = q)
y <- fetch_pubmed_data(x, format = "xml")
y
}