Check for key word in PubMed article titles

query PubMed

#Check pubmed article titles for a given year for a keyword (using partial matching).

library(XML)
library(stringr)


#get PubMed Ids for all journals for a given year
getPubMedIds<-function(year=2013, max=100){
  #max = maximum results to return
  url<-paste0("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=",year,"[PDAT]&RetMax=",max) 
	tmp<-readLines(url)
	doc<-xmlParse(tmp)	
	unlist(xmlToList(doc)$IdList)
}


# get article Titles
getArticleTitle<-function(id){
	unlist(sapply(1:length(id), function(i,pb = txtProgressBar(min = 0, max = length(id), style = 3)){
		url<-paste0("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=",id[i],"&retmode=XML&rettype=abstract")
		setTxtProgressBar(pb, i)
		tmp<-readLines(url)
		xml.data <- xmlParse(tmp)
		xmlToList(xml.data)$PubmedArticle$MedlineCitation$Article$ArticleTitle
	}))
}

# Check title for query term and return term
checkGetTerm<-function(obj,term){
	#obj is the object to check as a character vector
	#term is the query to do fuzzy matching on
	unlist(sapply(1:length(obj), function(i){
		tmp<-unlist(strsplit(obj[i]," "))
		id<-c(1:length(tmp))[!is.na(str_extract(tmp, term))]
		tmp[id]		
	}))
}


#EXAMPLE
#--------------------
#Get Article IDs
id<-getPubMedIds(year=2013, max=100)
#get article titles
obj<-getArticleTitle(id)
#check for term
checkGetTerm(obj,term="omics")