setwd("~/docs/jesse-go-ermineJ3")
library(rentrez)
pmids<-unique(read.table("Pub_ids_str.txt"))

getCiteCount<-function(pmid) {
  # don't spam Entrez
  Sys.sleep(runif(1)*2)
  
  # Fetch XML
  o<-entrez_link(db='pubmed', dbfrom='pubmed', retmode='xml', id=pmid, cmd='neighbor')$file
  
  # Grab field we want (as.numeric not really needed here)
  length(sapply(xpathApply(o, "//LinkSetDb[LinkName='pubmed_pubmed_citedin']/Link", xmlValue), as.numeric))
  
}

#example
getCiteCount(16007088)

#test
res<-sapply(pmids[1:2,], getCiteCount)
names(res)<-as.character(pmids[1:2,])

# reset and run for real.
res<-sapply(pmids[,1], getCiteCount)
names(res)<-pmids

write.table(res, file="Pub_ids_cites.txt", quote=F, sep='\t')