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## Define the class structure of the pubMedAbst object
setGeneric("pubMedAbst", function(object)
standardGeneric("pubMedAbst"))
setClass("pubMedAbst",
representation(pmid="character", authors="vector", abstText="character",
articleTitle="character", journal="character",
pubDate="character"))
setMethod("show", "pubMedAbst", function(object) {
s <- c("An object of class 'pubMedAbst':",
paste("Title: ", articleTitle(object)),
paste("PMID: ", pmid(object)),
paste("Authors:", paste(authors(object), collapse=", ")),
paste("Journal:", journal(object)),
paste("Date: ", pubDate(object)))
cat(strwrap(s, exdent=5), sep="\n")
})
## Define generics
if (is.null(getGeneric("authors")))
setGeneric("authors", function(object)
standardGeneric("authors"))
if (is.null(getGeneric("abstText")))
setGeneric("abstText", function(object)
standardGeneric("abstText"))
if (is.null(getGeneric("articleTitle")))
setGeneric("articleTitle", function(object)
standardGeneric("articleTitle"))
if (is.null(getGeneric("journal")))
setGeneric("journal", function(object)
standardGeneric("journal"))
if (is.null(getGeneric("pubDate")))
setGeneric("pubDate", function(object)
standardGeneric("pubDate"))
if (is.null(getGeneric("pmid")))
setGeneric("pmid", function(object)
standardGeneric("pmid"))
## Methods
setMethod("authors", "pubMedAbst", function(object)
object@authors)
setMethod("abstText", "pubMedAbst", function(object)
object@abstText)
setMethod("articleTitle", "pubMedAbst", function(object)
object@articleTitle)
setMethod("journal", "pubMedAbst", function(object)
object@journal)
setMethod("pubDate", "pubMedAbst", function(object)
object@pubDate)
setMethod("pmid", "pubMedAbst", function(object)
object@pmid)
buildPubMedAbst <- function(xml) {
## Passed in a XML tree detailing a single article
## will parse the XML and create a new class
xmlMedline <- xml["MedlineCitation"][[1]]
xmlArticle <- xmlMedline["Article"]
## Disable error messages, and wrap potential error causers
## w/ trys
options(show.error.messages = FALSE)
on.exit(options(show.error.messages=TRUE))
## Get the PMID
pmid <- xmlMedline["PMID"][[1]]
pmid <- try(as.character(xmlChildren(pmid)$text)[6])
if (inherits(pmid,"try-error") == TRUE) {
pmid <- "No PMID Provided"
}
## Retrieve Article Title
articleTitle <- xmlArticle[[1]][["ArticleTitle"]]
articleTitle <-
try(as.character(xmlChildren(articleTitle)$text)[6])
if (inherits(articleTitle,"try-error") == TRUE) {
articleTitle <- "No Title Provided"
}
## Retrieve the abstract
abstText <- xmlArticle[[1]]["Abstract"][[1]]["AbstractText"]
abstText <- try(as.character(xmlChildren(abstText[[1]])$text)[6])
if (inherits(abstText,"try-error") == TRUE) {
abstText <- "No Abstract Provided"
}
## Retrieve the date - get the year/month separately and then
## join them at the end. If no month or year provided, subst
## "MontH" and "Year" respectively
pubDateBase <-
xmlArticle[[1]]["Journal"][[1]]["JournalIssue"][[1]]["PubDate"]
pubDateMonth <- pubDateBase[[1]]["Month"]
pubDateMonth <-
try(as.character(xmlChildren(pubDateMonth[[1]])$text)[6])
if (inherits(pubDateMonth,"try-error") == TRUE) {
pubDateMonth <- "Month"
}
pubDateYear <- pubDateBase[[1]]["Year"]
pubDateYear <-
try(as.character(xmlChildren(pubDateYear[[1]])$text)[6])
if (inherits(pubDateYear, "try-error") == TRUE) {
pubDateYear <- "Year"
}
## Join up the date information
pubDate <- paste(pubDateMonth,pubDateYear)
## Get the journal this was published in
journal <-
xml["MedlineCitation"][[1]]["MedlineJournalInfo"][[1]]["MedlineTA"]
journal <- try(as.character(xmlChildren(journal[[1]])$text)[6])
if (inherits(journal,"try-error") == TRUE) {
journal <- "No Journal Provided"
}
## Build up a vector of author names, created by assembling the
## pieces of each author's name.
authorList <- xmlArticle[[1]]["AuthorList"]
authors <- vector()
numAuthors <- try(length(xmlChildren(authorList[[1]])))
if (inherits(numAuthors,"try-error") == TRUE) {
authors[1] <- "No Author Information Provided"
}
else {
for (i in 1:numAuthors) {
curAuthor <- authorList[[1]][i]
last <-
try(as.character(xmlChildren(curAuthor[[1]]["LastName"][[1]])$text)[6])
if (inherits(last,"try-error") == TRUE) {
last <- "LastName"
}
initial <-
try(as.character(xmlChildren(curAuthor[[1]]["Initials"][[1]])$text)[6])
if (inherits(initial,"try-error") == TRUE) {
initial <- "M"
}
authors[i] <- paste(initial,last)
}
}
## Restore error messages
options(show.error.messages=TRUE)
newPMA <- new("pubMedAbst", articleTitle=articleTitle,
abstText=abstText, pubDate=pubDate,authors=authors,
journal=journal, pmid=pmid)
return(newPMA)
}
pm.getabst <- function(geneids, basename) {
pmids <- getPMID(geneids, basename)
numids <- length(geneids)
rval <- vector("list", length=numids)
names(rval) <- geneids
for(i in 1:numids) {
pm <- pmids[[i]]
if( length(pm)==1 && is.na(pm) )
rval[[i]] <- NA
else {
absts <- pubmed(pm)
a <- xmlRoot(absts)
numAbst <- length(xmlChildren(a))
absts <- vector("list", length=numAbst)
for (j in 1:numAbst)
absts[[j]] <- buildPubMedAbst(a[[j]])
rval[[i]] <- absts
}
}
rval
}
pm.abstGrep <- function(pattern, absts, ...)
{
nabsts <- length(absts)
rval <- rep(FALSE, nabsts)
for(i in 1:nabsts) {
atxt <- abstText(absts[[i]])
ans <- grep(pattern, atxt, ...)
if( length(ans) && ans==1 )
rval[i] <- TRUE
}
rval
}
pm.titles <- function (absts) {
numa <- length(absts)
rval <- vector("list", length=numa)
for(j in 1:numa)
rval[[j]] <- sapply(absts[[j]], function(x) articleTitle(x))
rval
}
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