Query PubMed to retrieve counts of visualization papers* published in bioinformatics journals** between 2000 and 2015. (* = "visualization" in title or abstract, ** = Bioinformatics, BMC Bioinformatics, PLoS Computational Biology, Briefings in Bioinformatics)

pubmed_visualization_papers.R

require(RISmed);


queryPapers <- function(year, query="visualization") {
  query <- paste('((', query, '[Title/Abstract]) AND ("', year,'"[Date - Publication]) AND ("Bioinformatics (Oxford, England)"[Journal] OR "BMC bioinformatics"[Journal] OR "PLoS computational biology"[Journal] OR "Briefings in bioinformatics"[Journal]))', sep="")
  queryPubs <- EUtilsSummary(query, type='esearch', db='pubmed')

  all <- paste('(("', year,'"[Date - Publication]) AND ("Bioinformatics (Oxford, England)"[Journal] OR "BMC bioinformatics"[Journal] OR "PLoS computational biology"[Journal] OR "Briefings in bioinformatics"[Journal]))', sep="")
  allPubs <- EUtilsSummary('(("2015"[Date - Publication]) AND ("Bioinformatics (Oxford, England)"[Journal] OR "BMC bioinformatics"[Journal] OR "PLoS computational biology"[Journal] OR "Briefings in bioinformatics"[Journal]))', type='esearch', db='pubmed')

  return(list(queryPubs=queryPubs@count,allPubs=allPubs@count));
}

results <- matrix( NA, nrow=16, ncol=4 );
count <- 1;

for (y in 2000:2015) {
  result <- queryPapers(y);
  
  results[count,1] <- y;
  results[count,2] <- result$queryPubs;
  results[count,3] <- result$allPubs;
  results[count,4] <- result$queryPubs/result$allPubs * 100;  
  
  count <- count + 1;
}