easyPubMed (version 2.3)

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")

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").

Value

If format == "xml": a XMLInternalDocument-class object. For accessing these data, use a XML parser. If format != "xml": a "character" vector. Each element corresponds to one line of data.

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). 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 as a result of a fetch_pubmed_data() call).

References

http://www.biotechworld.it/bioinf/2016/01/05/querying-pubmed-via-the-easypubmed-package-in-r/ https://www.ncbi.nlm.nih.gov/books/NBK25499/table/chapter4.T._valid_values_of__retmode_and/

Examples

# NOT RUN {
# Example 01: retrieve data in XML format
dami_query_string <- "Damiano Fantini[AU]"
dami_on_pubmed <- get_pubmed_ids(dami_query_string)
dami_papers <- fetch_pubmed_data(dami_on_pubmed)
titles <- unlist(xpathApply(dami_papers, "//ArticleTitle", saveXML))
title_pos <- regexpr("<ArticleTitle>.*<\\/ArticleTitle>", titles)
titles <- substr(titles, title_pos + 14, title_pos + attributes(title_pos)$match.length - 16)
print(titles)
#
# }
# NOT RUN {
# Example 02: retrieve data in TXT format
dami_query_string <- "Damiano Fantini[AU]"
dami_on_pubmed <- get_pubmed_ids(dami_query_string)
dami_papers <- fetch_pubmed_data(dami_on_pubmed, format = "abstract")
dami_papers[dami_papers == ""] <- "\n"
cat(paste(dami_papers[1:65], collapse = ""))
# }