fetch_pubmed_data | R Documentation |
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.
fetch_pubmed_data(
pubmed_id_list,
retstart = 0,
retmax = 500,
format = "xml",
encoding = "UTF8",
api_key = NULL,
verbose = TRUE
)
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. |
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.
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.
Damiano Fantini damiano.fantini@gmail.com
https://www.data-pulse.com/dev_site/easypubmed/ https://www.ncbi.nlm.nih.gov/books/NBK25499/table/chapter4.T._valid_values_of__retmode_and/
## 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)
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