R/pubtator3_function.R

In pubmed.mineR: Text Mining of PubMed Abstracts

pubtator3_function = function (x) 
{
  test = getURL(paste("https://www.ncbi.nlm.nih.gov/research/pubtator3-api/publications/export/pubtator?pmids=", 
                      x, sep = ""))
  testa = unlist(strsplit(test, "\n", fixed = T))
  table1 = NULL
  for (i in 3:length(testa)) {
    temps = unlist(strsplit(testa[i], "\t", fixed = T))
    if (length(temps) == 5) {
      temps = c(temps, "No Data")
    }
    table1 = rbind(table1, temps)
  }
  if (ncol(table1) == 6) {
    table2 = table1
    colnames(table2) = c("PMID", "Start", "End", "Term", 
                         "TermType", "TermID")
    gene = NULL
    disease = NULL
    mutation = NULL
    chemical = NULL
    species = NULL
    for (i in 1:length(table2[, 5])) {
      if (table2[i, 5] == "Gene") 
        gene = c(gene, paste(table2[i, 4], table2[i, 
                                                  6], sep = ">"))
      else if (table2[i, 5] == "Disease") 
        disease = c(disease, paste(table2[i, 4], table2[i, 
                                                        6], sep = ">"))
      else if (table2[i, 5] == "Mutation") 
        mutation = c(mutation, paste(table2[i, 4], table2[i, 
                                                          6], sep = ">"))
      else if (table2[i, 5] == "Chemical") 
        chemical = c(chemical, paste(table2[i, 4], table2[i, 
                                                          6], sep = ">"))
      else if (table2[i, 5] == "Species") 
        species = c(species, paste(table2[i, 4], table2[i, 
                                                        6], sep = ">"))
    }
    gene = union(gene, gene)
    disease = union(disease, disease)
    mutation = union(mutation, mutation)
    chemical = union(chemical, chemical)
    species = union(species, species)
    return(list(Genes = gene, Diseases = disease, Mutations = mutation, 
                Chemicals = chemical, Species = species, PMID = x))
  }
  else return(" No Data ")
}