fetch_pubmed_data: Retrieve PubMed Data in XML or TXT Format

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

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
)

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.

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 the second half of 2024.

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.

Author(s)

Damiano Fantini [e-mail]

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)

## Not run: 
## 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

## End(Not run)

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