fetch_pubmed_data {easyPubMed}

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")

Arguments

pubmed_id_list

List: the result of a get_pubmed_ids() call.

retstart

Integer (>=0): index of the first UID in the retrieved PubMed Search Result set to be included in the output (default=0, corresponding to the first record of the entire set).

retmax

Integer (>=1): size of the batch of PubMed records to be retrieved at one time.

format

Character: element specifying the output format. The following values are allowed: c("asn.1", "xml", "medline", "uilist", "abstract").

encoding

The encoding of an input/output connection can be specified by name (for example, "ASCII", or "UTF-8", in the same way as it would be given to the function base::iconv(). See iconv() help page for how to find out more about encodings that can be used on your platform. Here, we recommend using "UTF-8".

Details

Retrieve PubMed records based on the results of a get_pubmed_ids() query. Records are retrieved from Entrez via the PubMed API efetch function. The first entry to be retrieved may be adjusted via the retastart parameter (this allows the user to download large batches of PubMed data in multiple runs). The maximum number of entries to be retrieved can also be set adjusting the retmax parameter (1 < retmax < 5000). Data will be downloaded on the fly (no files are saved locally).

Value

An object (vector) of class "character". If format is set to "xml" (default), a single String including all PubMed records (with XML tags embedded) is returned. If a different format is selected, a vector of strings is returned, where each row 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

try({ 
  ## Example 01: retrieve data in TXT format
  library("easyPubMed")
  dami_query_string <- "Damiano Fantini[AU] AND 2018[PDAT]"
  dami_on_pubmed <- get_pubmed_ids(dami_query_string)
  Sys.sleep(1) # avoid server timeout
  dami_papers <- fetch_pubmed_data(dami_on_pubmed, format = "abstract")
  dami_papers[dami_papers == ""] <- "\n"
  cat(paste(dami_papers[1:65], collapse = ""))
}, silent = TRUE)

## Not run: 
## Example 02: retrieve data in XML format
library("easyPubMed")
dami_query_string <- "Damiano Fantini[AU]"
dami_on_pubmed <- get_pubmed_ids(dami_query_string)
dami_papers <- fetch_pubmed_data(dami_on_pubmed)
titles <- custom_grep(dami_papers, "ArticleTitle", "char")
print(titles)

## End(Not run)