#' Adapted from PubMedWordCloud to work with compMS2Miner
#' @param PMID character vector of pubMed ids to get abstracts for.
#' @details if the query sequence is too long than 500 this function will not work
#' @export
getAbs <- function(PMID){
if(!require(XML)){
stop('The XML package is required to use this function')
}
if(length(PMID) > 500){
stop('The maximum PMID length is 500')
}
if (length(PMID) > 0) {
eDDownload <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id="
hlp1 <- paste(eDDownload, paste(PMID, collapse = ",",
sep = ""), sep = "")
hlp2 <- paste(hlp1, "&rettype=abstract", sep = "")
hlpURL <- RCurl::getURL(hlp2, .opts=RCurl::curlOptions(followlocation=TRUE))
testDoc <- XML::xmlTreeParse(hlpURL, useInternalNodes = TRUE)
topFetch <- XML::xmlRoot(testDoc)
abst <- XML::xpathSApply(topFetch, "//Abstract", xmlValue)
}
else {
abst = c("Zero", "Articles", "Found")
}
return(abst)
} # end function
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