example-runner.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "import json, pandas as pd"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Run the CaseOLAP Pipeline"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Server-Wide Steps\n",
    "Steps 1-5 should be performed once and is used globally, across the whole server. The later steps should be customized for each project"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 1. Download the documents"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Downloading baseline files from ftp://ftp.ncbi.nlm.nih.gov/pubmed/baseline/ For details, see the download logfile\n",
      "Finished downloading PubMed baseline files. 3s\n",
      "Downloading update files from ftp://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/ For details, see the download logfile\n",
      "Finished downloading PubMed update files.1.3055191040039062\n",
      "==== Start checking md5 in ./ftp.ncbi.nlm.nih.gov/pubmed/baseline/ ====\n",
      "100 files checked\n",
      "200 files checked\n",
      "300 files checked\n",
      "400 files checked\n",
      "500 files checked\n",
      "600 files checked\n",
      "700 files checked\n",
      "800 files checked\n",
      "900 files checked\n",
      "1000 files checked\n",
      "1100 files checked\n",
      "\n",
      "==== All md5 checks succeeded (1114 files) ====\n",
      "==== Start checking md5 in ./ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/ ====\n",
      "100 files checked\n",
      "200 files checked\n",
      "300 files checked\n",
      "\n",
      "==== All md5 checks succeeded (314 files) ====\n",
      "==== Start extracting in ./ftp.ncbi.nlm.nih.gov/pubmed/baseline/ ====\n",
      "50 files extracted,77.79513263702393 seconds\n",
      "100 files extracted,155.49333715438843 seconds\n",
      "150 files extracted,228.6057960987091 seconds\n",
      "200 files extracted,306.2978663444519 seconds\n",
      "250 files extracted,389.874459028244 seconds\n",
      "300 files extracted,462.0407512187958 seconds\n",
      "350 files extracted,541.7054972648621 seconds\n",
      "400 files extracted,622.4119820594788 seconds\n",
      "450 files extracted,703.2535281181335 seconds\n",
      "500 files extracted,779.548348903656 seconds\n",
      "550 files extracted,848.6742653846741 seconds\n",
      "600 files extracted,933.0440466403961 seconds\n",
      "650 files extracted,1017.8795697689056 seconds\n",
      "700 files extracted,1098.5770461559296 seconds\n",
      "750 files extracted,1183.0506687164307 seconds\n",
      "800 files extracted,1264.5244987010956 seconds\n",
      "850 files extracted,1346.6578576564789 seconds\n",
      "900 files extracted,1423.6081507205963 seconds\n",
      "950 files extracted,1494.790334224701 seconds\n",
      "1000 files extracted,1571.1628241539001 seconds\n",
      "1050 files extracted,1650.2064697742462 seconds\n",
      "1100 files extracted,1730.5639734268188 seconds\n",
      "==== All files extracted (1114 files). Total time: 1753.0422735214233 ====\n",
      "==== Start extracting in ./ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/ ====\n",
      "50 files extracted,90.97581577301025 seconds\n",
      "100 files extracted,173.5305414199829 seconds\n",
      "150 files extracted,263.80849528312683 seconds\n",
      "200 files extracted,355.54834151268005 seconds\n",
      "250 files extracted,440.880898475647 seconds\n",
      "300 files extracted,539.3024826049805 seconds\n",
      "==== All files extracted (314 files). Total time: 561.8892738819122 ====\n"
     ]
    }
   ],
   "source": [
    "!python '01_run_download.py'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 2. Parse the documents\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'title': True, 'PMID': True, 'author': False, 'abstract': True, 'MeSH': True, 'location': True, 'date': True, 'journal': True, 'full_text': True}\n",
      "Parsing baseline containing 1114 bulk files\n",
      "==================================================\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.836343765258789\n",
      "Parsing 1/1114 from baseline:pubmed22n0100.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.532426118850708\n",
      "Parsing 2/1114 from baseline:pubmed22n0918.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.053693771362305\n",
      "Parsing 3/1114 from baseline:pubmed22n0425.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.248413324356079\n",
      "Parsing 4/1114 from baseline:pubmed22n0395.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.04988694190979\n",
      "Parsing 5/1114 from baseline:pubmed22n1062.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.014681816101074\n",
      "Parsing 6/1114 from baseline:pubmed22n0549.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.252095460891724\n",
      "Parsing 7/1114 from baseline:pubmed22n0737.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 5.790035247802734\n",
      "Parsing 8/1114 from baseline:pubmed22n0578.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.760958909988403\n",
      "Parsing 9/1114 from baseline:pubmed22n0835.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.652023792266846\n",
      "Parsing 10/1114 from baseline:pubmed22n0324.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.083364248275757\n",
      "Parsing 11/1114 from baseline:pubmed22n1015.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.787740707397461\n",
      "Parsing 12/1114 from baseline:pubmed22n0663.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.879054307937622\n",
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      "Parsing finished. 29999 articles parsed.Total time: 10.53443169593811\n",
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      "Parsing finished. 29999 articles parsed.Total time: 12.241492509841919\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.557954549789429\n",
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      "Parsing finished. 29999 articles parsed.Total time: 7.51203989982605\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.93821907043457\n",
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      "Parsing finished. 29999 articles parsed.Total time: 5.611681222915649\n",
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      "Parsing finished. 29999 articles parsed.Total time: 7.430776119232178\n",
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      "Parsing finished. 29999 articles parsed.Total time: 6.283663511276245\n",
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      "Parsing finished. 29999 articles parsed.Total time: 6.282581090927124\n",
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      "Parsing finished. 29999 articles parsed.Total time: 8.07344913482666\n",
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      "Parsing finished. 29999 articles parsed.Total time: 9.59392762184143\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.888127565383911\n",
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      "Parsing finished. 29999 articles parsed.Total time: 6.249664068222046\n",
      "Parsing 28/1114 from baseline:pubmed22n0456.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.43532419204712\n",
      "Parsing 29/1114 from baseline:pubmed22n0794.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.233983993530273\n",
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      "Parsing finished. 29999 articles parsed.Total time: 9.972118854522705\n",
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      "Parsing finished. 29999 articles parsed.Total time: 12.379710674285889\n",
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      "Parsing finished. 29999 articles parsed.Total time: 7.993685007095337\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.431192874908447\n",
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      "Parsing finished. 29999 articles parsed.Total time: 6.259878396987915\n",
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      "Parsing finished. 29999 articles parsed.Total time: 9.792199611663818\n",
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      "Parsing finished. 29999 articles parsed.Total time: 9.840229749679565\n",
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      "Parsing finished. 29999 articles parsed.Total time: 8.481181859970093\n",
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      "Parsing finished. 15862 articles parsed.Total time: 4.615276336669922\n",
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      "Parsing finished. 29999 articles parsed.Total time: 10.048155546188354\n",
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      "Parsing finished. 29999 articles parsed.Total time: 10.426165103912354\n",
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      "Parsing finished. 29999 articles parsed.Total time: 10.909175395965576\n",
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      "Parsing finished. 29999 articles parsed.Total time: 7.8452911376953125\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.64866828918457\n",
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      "Parsing finished. 29999 articles parsed.Total time: 9.535674810409546\n",
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      "Parsing finished. 29999 articles parsed.Total time: 9.992316246032715\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.895882844924927\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.854485034942627\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.367040634155273\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.131513595581055\n",
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      "Parsing finished. 29999 articles parsed.Total time: 8.302735567092896\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.938210248947144\n",
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      "Parsing finished. 29999 articles parsed.Total time: 8.671122789382935\n",
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      "Parsing finished. 29999 articles parsed.Total time: 7.469512701034546\n",
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      "Parsing finished. 29999 articles parsed.Total time: 9.590963363647461\n",
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      "Parsing finished. 29999 articles parsed.Total time: 9.860940217971802\n",
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      "Parsing finished. 29999 articles parsed.Total time: 12.23062801361084\n",
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      "Parsing finished. 29999 articles parsed.Total time: 6.359020471572876\n",
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      "Parsing finished. 29999 articles parsed.Total time: 9.768045425415039\n",
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      "Parsing finished. 29999 articles parsed.Total time: 10.847849130630493\n",
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      "Parsing finished. 29999 articles parsed.Total time: 7.532160520553589\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.8410005569458\n",
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      "Parsing finished. 29999 articles parsed.Total time: 12.772412538528442\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.275387048721313\n",
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      "Parsing finished. 29999 articles parsed.Total time: 8.66999864578247\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.610639333724976\n",
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      "Parsing finished. 29999 articles parsed.Total time: 8.095463275909424\n",
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      "Parsing finished. 29999 articles parsed.Total time: 8.233505964279175\n",
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      "Parsing finished. 29999 articles parsed.Total time: 9.774132251739502\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.460297107696533\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.396536827087402\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.106424331665039\n",
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      "Parsing finished. 29999 articles parsed.Total time: 8.760009765625\n",
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      "Parsing finished. 29999 articles parsed.Total time: 7.788755893707275\n",
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      "Parsing finished. 29999 articles parsed.Total time: 9.591689109802246\n",
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      "Parsing finished. 29999 articles parsed.Total time: 6.405556917190552\n",
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      "Parsing finished. 29999 articles parsed.Total time: 12.432202339172363\n",
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      "Parsing finished. 29999 articles parsed.Total time: 8.167948007583618\n",
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      "Parsing finished. 29999 articles parsed.Total time: 7.713397264480591\n",
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      "Parsing finished. 29999 articles parsed.Total time: 12.275278806686401\n",
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      "Parsing finished. 29999 articles parsed.Total time: 10.16543960571289\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.765599489212036\n",
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      "Parsing finished. 29999 articles parsed.Total time: 12.290774822235107\n",
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      "Parsing finished. 29999 articles parsed.Total time: 12.771489143371582\n",
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      "Parsing finished. 29999 articles parsed.Total time: 6.950173377990723\n",
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      "Parsing finished. 29999 articles parsed.Total time: 9.814867973327637\n",
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      "Parsing finished. 29999 articles parsed.Total time: 9.819813251495361\n",
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      "Parsing finished. 29999 articles parsed.Total time: 8.589284896850586\n",
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      "Parsing finished. 29999 articles parsed.Total time: 8.795319557189941\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.66805911064148\n",
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      "Parsing finished. 29999 articles parsed.Total time: 12.632461547851562\n",
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      "Parsing finished. 29999 articles parsed.Total time: 10.081488609313965\n",
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      "Parsing finished. 29999 articles parsed.Total time: 10.066141843795776\n",
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      "Parsing finished. 29999 articles parsed.Total time: 9.58857774734497\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.365687131881714\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.549057006835938\n",
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      "Parsing finished. 29999 articles parsed.Total time: 12.423521757125854\n",
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      "Parsing finished. 29999 articles parsed.Total time: 7.399087429046631\n",
      "Parsing 366/1114 from baseline:pubmed22n0191.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.540525197982788\n",
      "Parsing 367/1114 from baseline:pubmed22n0602.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.813173055648804\n",
      "Parsing 368/1114 from baseline:pubmed22n0544.xml\n",
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      "Parsing 371/1114 from baseline:pubmed22n0599.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.89884352684021\n",
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      "Parsing finished. 29999 articles parsed.Total time: 10.328274726867676\n",
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      "Parsing finished. 29999 articles parsed.Total time: 6.324582815170288\n",
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      "Parsing finished. 29999 articles parsed.Total time: 10.237125158309937\n",
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      "Parsing finished. 29999 articles parsed.Total time: 9.923420190811157\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.635704755783081\n",
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      "Parsing finished. 29999 articles parsed.Total time: 8.611736536026001\n",
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      "Parsing finished. 29999 articles parsed.Total time: 12.864211082458496\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.985514879226685\n",
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      "Parsing finished. 29999 articles parsed.Total time: 7.7469093799591064\n",
      "Parsing 384/1114 from baseline:pubmed22n0128.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.60719609260559\n",
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      "Parsing finished. 29999 articles parsed.Total time: 10.338652849197388\n",
      "Parsing 386/1114 from baseline:pubmed22n0494.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.589876413345337\n",
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      "Parsing finished. 29999 articles parsed.Total time: 10.02063798904419\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.271026134490967\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.81432032585144\n",
      "Parsing 390/1114 from baseline:pubmed22n0856.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.832191944122314\n",
      "Parsing 391/1114 from baseline:pubmed22n0613.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.660783290863037\n",
      "Parsing 392/1114 from baseline:pubmed22n0074.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.196280717849731\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.103466749191284\n",
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      "Parsing finished. 29999 articles parsed.Total time: 9.63030219078064\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.400328636169434\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.365132570266724\n",
      "Parsing 397/1114 from baseline:pubmed22n0711.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.548710584640503\n",
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      "Parsing finished. 29999 articles parsed.Total time: 12.40348768234253\n",
      "Parsing 399/1114 from baseline:pubmed22n1066.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.410631895065308\n",
      "Parsing 400/1114 from baseline:pubmed22n0338.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.712951183319092\n",
      "Parsing 401/1114 from baseline:pubmed22n1034.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.358643293380737\n",
      "Parsing 402/1114 from baseline:pubmed22n1023.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.715683698654175\n",
      "Parsing 403/1114 from baseline:pubmed22n0863.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.096954345703125\n",
      "Parsing 404/1114 from baseline:pubmed22n0855.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 5.889015436172485\n",
      "Parsing 405/1114 from baseline:pubmed22n0332.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.600082397460938\n",
      "Parsing 406/1114 from baseline:pubmed22n1022.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.707634687423706\n",
      "Parsing 407/1114 from baseline:pubmed22n0597.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.64037823677063\n",
      "Parsing 408/1114 from baseline:pubmed22n0188.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.632107257843018\n",
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      "Parsing finished. 29999 articles parsed.Total time: 9.824100732803345\n",
      "Parsing 410/1114 from baseline:pubmed22n0405.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.119179725646973\n",
      "Parsing 411/1114 from baseline:pubmed22n0500.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.463483810424805\n",
      "Parsing 412/1114 from baseline:pubmed22n0680.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.421542644500732\n",
      "Parsing 413/1114 from baseline:pubmed22n1003.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.853049278259277\n",
      "Parsing 414/1114 from baseline:pubmed22n0924.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.41140604019165\n",
      "Parsing 415/1114 from baseline:pubmed22n0437.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.649237155914307\n",
      "Parsing 416/1114 from baseline:pubmed22n0526.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.704242944717407\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.302293300628662\n",
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      "Parsing finished. 29999 articles parsed.Total time: 8.28371810913086\n",
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      "Parsing finished. 29999 articles parsed.Total time: 7.963954925537109\n",
      "Parsing 420/1114 from baseline:pubmed22n0165.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.609058141708374\n",
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      "Parsing finished. 29999 articles parsed.Total time: 12.406579494476318\n",
      "Parsing 422/1114 from baseline:pubmed22n1060.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.357221841812134\n",
      "Parsing 423/1114 from baseline:pubmed22n0334.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.334084510803223\n",
      "Parsing 424/1114 from baseline:pubmed22n0222.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.393136739730835\n",
      "Parsing 425/1114 from baseline:pubmed22n0520.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.736637115478516\n",
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      "Parsing finished. 29999 articles parsed.Total time: 10.810158014297485\n",
      "Parsing 427/1114 from baseline:pubmed22n0562.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.327289581298828\n",
      "Parsing 428/1114 from baseline:pubmed22n0431.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.347029685974121\n",
      "Parsing 429/1114 from baseline:pubmed22n0070.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.778507232666016\n",
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      "Parsing finished. 29999 articles parsed.Total time: 6.9476213455200195\n",
      "Parsing 431/1114 from baseline:pubmed22n0150.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.280814409255981\n",
      "Parsing 432/1114 from baseline:pubmed22n0563.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.443058967590332\n",
      "Parsing 433/1114 from baseline:pubmed22n0208.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.874023199081421\n",
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      "Parsing finished. 29999 articles parsed.Total time: 9.89821481704712\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.692859411239624\n",
      "Parsing 436/1114 from baseline:pubmed22n0898.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.504107475280762\n",
      "Parsing 437/1114 from baseline:pubmed22n0539.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.007778644561768\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.731860637664795\n",
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      "Parsing finished. 29999 articles parsed.Total time: 10.269717931747437\n",
      "Parsing 440/1114 from baseline:pubmed22n0509.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.04620623588562\n",
      "Parsing 441/1114 from baseline:pubmed22n0982.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.609073162078857\n",
      "Parsing 442/1114 from baseline:pubmed22n0005.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 5.998855352401733\n",
      "Parsing 443/1114 from baseline:pubmed22n0173.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.677980899810791\n",
      "Parsing 444/1114 from baseline:pubmed22n0220.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.130377769470215\n",
      "Parsing 445/1114 from baseline:pubmed22n0422.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.853567361831665\n",
      "Parsing 446/1114 from baseline:pubmed22n0320.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.869619607925415\n",
      "Parsing 447/1114 from baseline:pubmed22n0002.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.648640394210815\n",
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      "Parsing finished. 29999 articles parsed.Total time: 7.218714952468872\n",
      "Parsing 449/1114 from baseline:pubmed22n0187.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.332677125930786\n",
      "Parsing 450/1114 from baseline:pubmed22n0515.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.272701263427734\n",
      "Parsing 451/1114 from baseline:pubmed22n0008.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.26580262184143\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.393409967422485\n",
      "Parsing 453/1114 from baseline:pubmed22n1104.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.67736005783081\n",
      "Parsing 454/1114 from baseline:pubmed22n1008.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.365066766738892\n",
      "Parsing 455/1114 from baseline:pubmed22n0535.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.747981071472168\n",
      "Parsing 456/1114 from baseline:pubmed22n1048.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.988821983337402\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.951268672943115\n",
      "Parsing 458/1114 from baseline:pubmed22n0959.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.621654748916626\n",
      "Parsing 459/1114 from baseline:pubmed22n0470.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.691906690597534\n",
      "Parsing 460/1114 from baseline:pubmed22n0060.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.96064281463623\n",
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      "Parsing finished. 29999 articles parsed.Total time: 9.732095956802368\n",
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      "Parsing finished. 29999 articles parsed.Total time: 7.404444456100464\n",
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      "Parsing finished. 29999 articles parsed.Total time: 10.29560661315918\n",
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      "Parsing finished. 29999 articles parsed.Total time: 9.962568044662476\n",
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      "Parsing finished. 29999 articles parsed.Total time: 12.032570838928223\n",
      "Parsing 466/1114 from baseline:pubmed22n0986.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.165099859237671\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.517085552215576\n",
      "Parsing 468/1114 from baseline:pubmed22n0719.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.697873830795288\n",
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      "Parsing finished. 29999 articles parsed.Total time: 8.25623083114624\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.430237293243408\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.117873907089233\n",
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      "Parsing finished. 29999 articles parsed.Total time: 9.902401208877563\n",
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      "Parsing finished. 29999 articles parsed.Total time: 12.259934663772583\n",
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      "Parsing finished. 29999 articles parsed.Total time: 10.436192512512207\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.038706302642822\n",
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      "Parsing finished. 29999 articles parsed.Total time: 9.837593793869019\n",
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      "Parsing finished. 29999 articles parsed.Total time: 9.562390804290771\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.746340274810791\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.606314897537231\n",
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      "Parsing finished. 29999 articles parsed.Total time: 9.68692421913147\n",
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      "Parsing finished. 29999 articles parsed.Total time: 10.545128345489502\n",
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      "Parsing finished. 29999 articles parsed.Total time: 10.395479440689087\n",
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      "Parsing finished. 29999 articles parsed.Total time: 10.817992687225342\n",
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      "Parsing finished. 29999 articles parsed.Total time: 9.858856678009033\n",
      "Parsing 486/1114 from baseline:pubmed22n0400.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.000993728637695\n",
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      "Parsing finished. 29999 articles parsed.Total time: 9.34008240699768\n",
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      "Parsing finished. 29999 articles parsed.Total time: 9.992617845535278\n",
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      "Parsing finished. 29999 articles parsed.Total time: 10.104774713516235\n",
      "Parsing 490/1114 from baseline:pubmed22n0540.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.969855070114136\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.733537673950195\n",
      "Parsing 492/1114 from baseline:pubmed22n0770.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.157307386398315\n",
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      "Parsing finished. 29999 articles parsed.Total time: 11.882938861846924\n",
      "Parsing 494/1114 from baseline:pubmed22n0802.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.41892147064209\n",
      "Parsing 495/1114 from baseline:pubmed22n0108.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.811886310577393\n",
      "Parsing 496/1114 from baseline:pubmed22n0886.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.882099628448486\n",
      "Parsing 497/1114 from baseline:pubmed22n0795.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.393686771392822\n",
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      "Parsing finished. 29999 articles parsed.Total time: 9.78861117362976\n",
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      "Parsing finished. 29999 articles parsed.Total time: 8.899851322174072\n",
      "Parsing 500/1114 from baseline:pubmed22n0140.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.410969972610474\n",
      "Parsing 501/1114 from baseline:pubmed22n0278.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.496687889099121\n",
      "Parsing 502/1114 from baseline:pubmed22n0550.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.804680347442627\n",
      "Parsing 503/1114 from baseline:pubmed22n1100.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.410529136657715\n",
      "Parsing 504/1114 from baseline:pubmed22n0575.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.860733032226562\n",
      "Parsing 505/1114 from baseline:pubmed22n0226.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.405235767364502\n",
      "Parsing 506/1114 from baseline:pubmed22n0529.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.026221752166748\n",
      "Parsing 507/1114 from baseline:pubmed22n0032.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.497279405593872\n",
      "Parsing 508/1114 from baseline:pubmed22n1054.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.094032287597656\n",
      "Parsing 509/1114 from baseline:pubmed22n0415.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.840051174163818\n",
      "Parsing 510/1114 from baseline:pubmed22n0847.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.586764335632324\n",
      "Parsing 511/1114 from baseline:pubmed22n1018.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.042295455932617\n",
      "Parsing 512/1114 from baseline:pubmed22n0305.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.567484378814697\n",
      "Parsing 513/1114 from baseline:pubmed22n0003.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.999497175216675\n",
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      "Parsing finished. 29999 articles parsed.Total time: 12.691455125808716\n",
      "Parsing 515/1114 from baseline:pubmed22n1030.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.058406114578247\n",
      "Parsing 516/1114 from baseline:pubmed22n0199.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.470107316970825\n",
      "Parsing 517/1114 from baseline:pubmed22n0875.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.580685138702393\n",
      "Parsing 518/1114 from baseline:pubmed22n0725.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.186095952987671\n",
      "Parsing 519/1114 from baseline:pubmed22n0015.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.812593460083008\n",
      "Parsing 520/1114 from baseline:pubmed22n0787.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.566080808639526\n",
      "Parsing 521/1114 from baseline:pubmed22n0656.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.141390562057495\n",
      "Parsing 522/1114 from baseline:pubmed22n0505.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.382567882537842\n",
      "Parsing 523/1114 from baseline:pubmed22n1009.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.363327741622925\n",
      "Parsing 524/1114 from baseline:pubmed22n0440.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.543017148971558\n",
      "Parsing 525/1114 from baseline:pubmed22n0133.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.444541931152344\n",
      "Parsing 526/1114 from baseline:pubmed22n0612.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.41968584060669\n",
      "Parsing 527/1114 from baseline:pubmed22n1099.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.062288522720337\n",
      "Parsing 528/1114 from baseline:pubmed22n0479.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.044564723968506\n",
      "Parsing 529/1114 from baseline:pubmed22n0815.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.161123275756836\n",
      "Parsing 530/1114 from baseline:pubmed22n0530.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.35528039932251\n",
      "Parsing 531/1114 from baseline:pubmed22n0970.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.329521179199219\n",
      "Parsing 532/1114 from baseline:pubmed22n0474.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.878402948379517\n",
      "Parsing 533/1114 from baseline:pubmed22n0905.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.095414161682129\n",
      "Parsing 534/1114 from baseline:pubmed22n0406.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.048177480697632\n",
      "Parsing 535/1114 from baseline:pubmed22n0098.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.881190776824951\n",
      "Parsing 536/1114 from baseline:pubmed22n0628.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.468369245529175\n",
      "Parsing 537/1114 from baseline:pubmed22n0991.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.839673280715942\n",
      "Parsing 538/1114 from baseline:pubmed22n0379.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.586626768112183\n",
      "Parsing 539/1114 from baseline:pubmed22n1038.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.328864574432373\n",
      "Parsing 540/1114 from baseline:pubmed22n1063.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.33180022239685\n",
      "Parsing 541/1114 from baseline:pubmed22n1109.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.853679418563843\n",
      "Parsing 542/1114 from baseline:pubmed22n0901.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.864124059677124\n",
      "Parsing 543/1114 from baseline:pubmed22n1041.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 5.615064382553101\n",
      "Parsing 544/1114 from baseline:pubmed22n0645.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.704692125320435\n",
      "Parsing 545/1114 from baseline:pubmed22n0274.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.74625301361084\n",
      "Parsing 546/1114 from baseline:pubmed22n1036.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.954927921295166\n",
      "Parsing 547/1114 from baseline:pubmed22n0606.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.947962999343872\n",
      "Parsing 548/1114 from baseline:pubmed22n1080.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.87432599067688\n",
      "Parsing 549/1114 from baseline:pubmed22n0254.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.054379224777222\n",
      "Parsing 550/1114 from baseline:pubmed22n0348.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.908361434936523\n",
      "Parsing 551/1114 from baseline:pubmed22n0899.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.851337432861328\n",
      "Parsing 552/1114 from baseline:pubmed22n0313.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.392312049865723\n",
      "Parsing 553/1114 from baseline:pubmed22n0777.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.133472442626953\n",
      "Parsing 554/1114 from baseline:pubmed22n0967.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.391478061676025\n",
      "Parsing 555/1114 from baseline:pubmed22n0584.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.526756525039673\n",
      "Parsing 556/1114 from baseline:pubmed22n0768.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.12091851234436\n",
      "Parsing 557/1114 from baseline:pubmed22n0407.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.820246934890747\n",
      "Parsing 558/1114 from baseline:pubmed22n0353.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.786449909210205\n",
      "Parsing 559/1114 from baseline:pubmed22n0299.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.410547256469727\n",
      "Parsing 560/1114 from baseline:pubmed22n0101.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.359631538391113\n",
      "Parsing 561/1114 from baseline:pubmed22n0277.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.627707481384277\n",
      "Parsing 568/1114 from baseline:pubmed22n0762.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 13.474847555160522\n",
      "Parsing 569/1114 from baseline:pubmed22n1078.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.666284799575806\n",
      "Parsing 570/1114 from baseline:pubmed22n0004.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.852184295654297\n",
      "Parsing 571/1114 from baseline:pubmed22n0477.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.149438619613647\n",
      "Parsing 572/1114 from baseline:pubmed22n0603.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.392555952072144\n",
      "Parsing 573/1114 from baseline:pubmed22n0063.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.090369701385498\n",
      "Parsing 574/1114 from baseline:pubmed22n0469.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.840494394302368\n",
      "Parsing 575/1114 from baseline:pubmed22n0755.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.204529762268066\n",
      "Parsing 576/1114 from baseline:pubmed22n0428.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.507310152053833\n",
      "Parsing 577/1114 from baseline:pubmed22n0593.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.420125246047974\n",
      "Parsing 578/1114 from baseline:pubmed22n1071.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.807243347167969\n",
      "Parsing 579/1114 from baseline:pubmed22n0889.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.46278691291809\n",
      "Parsing 580/1114 from baseline:pubmed22n0556.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.624077558517456\n",
      "Parsing 581/1114 from baseline:pubmed22n0941.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.283760786056519\n",
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      "Parsing finished. 29999 articles parsed.Total time: 10.690415859222412\n",
      "Parsing 583/1114 from baseline:pubmed22n0657.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.922430753707886\n",
      "Parsing 584/1114 from baseline:pubmed22n0419.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.79056167602539\n",
      "Parsing 585/1114 from baseline:pubmed22n0951.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.942482233047485\n",
      "Parsing 586/1114 from baseline:pubmed22n0163.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.742083549499512\n",
      "Parsing 587/1114 from baseline:pubmed22n0960.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.56226372718811\n",
      "Parsing 588/1114 from baseline:pubmed22n0132.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.324296474456787\n",
      "Parsing 589/1114 from baseline:pubmed22n0012.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.728282690048218\n",
      "Parsing 590/1114 from baseline:pubmed22n0097.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.702517986297607\n",
      "Parsing 591/1114 from baseline:pubmed22n1110.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.025900840759277\n",
      "Parsing 592/1114 from baseline:pubmed22n0130.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.555824041366577\n",
      "Parsing 593/1114 from baseline:pubmed22n0769.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.545517683029175\n",
      "Parsing 594/1114 from baseline:pubmed22n0709.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.194862604141235\n",
      "Parsing 595/1114 from baseline:pubmed22n0731.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.948773622512817\n",
      "Parsing 596/1114 from baseline:pubmed22n0374.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.796579122543335\n",
      "Parsing 597/1114 from baseline:pubmed22n0980.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.146347999572754\n",
      "Parsing 598/1114 from baseline:pubmed22n0245.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.640025615692139\n",
      "Parsing 599/1114 from baseline:pubmed22n1012.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.897947072982788\n",
      "Parsing 600/1114 from baseline:pubmed22n0383.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.932576656341553\n",
      "Parsing 601/1114 from baseline:pubmed22n0834.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.75645637512207\n",
      "Parsing 602/1114 from baseline:pubmed22n0105.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.69624137878418\n",
      "Parsing 603/1114 from baseline:pubmed22n0076.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.060038328170776\n",
      "Parsing 604/1114 from baseline:pubmed22n0573.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.291258096694946\n",
      "Parsing 605/1114 from baseline:pubmed22n0473.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 5.8214874267578125\n",
      "Parsing 606/1114 from baseline:pubmed22n0611.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.39574670791626\n",
      "Parsing 607/1114 from baseline:pubmed22n1028.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.834580898284912\n",
      "Parsing 608/1114 from baseline:pubmed22n0392.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.546709060668945\n",
      "Parsing 609/1114 from baseline:pubmed22n0134.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.820290565490723\n",
      "Parsing 610/1114 from baseline:pubmed22n0853.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.526978492736816\n",
      "Parsing 611/1114 from baseline:pubmed22n1040.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.068999528884888\n",
      "Parsing 612/1114 from baseline:pubmed22n0495.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.236837387084961\n",
      "Parsing 613/1114 from baseline:pubmed22n0472.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.654608964920044\n",
      "Parsing 614/1114 from baseline:pubmed22n0027.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.398332595825195\n",
      "Parsing 615/1114 from baseline:pubmed22n0106.xml\n",
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      "Parsing 616/1114 from baseline:pubmed22n0692.xml\n",
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      "Parsing 617/1114 from baseline:pubmed22n0605.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.383952379226685\n",
      "Parsing 618/1114 from baseline:pubmed22n0708.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.668948411941528\n",
      "Parsing 619/1114 from baseline:pubmed22n0739.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.862895488739014\n",
      "Parsing 620/1114 from baseline:pubmed22n0879.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.866045475006104\n",
      "Parsing 621/1114 from baseline:pubmed22n0285.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.040735721588135\n",
      "Parsing 622/1114 from baseline:pubmed22n0029.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.18588638305664\n",
      "Parsing 623/1114 from baseline:pubmed22n0987.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.309724569320679\n",
      "Parsing 624/1114 from baseline:pubmed22n0432.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.708455085754395\n",
      "Parsing 625/1114 from baseline:pubmed22n0618.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.265912771224976\n",
      "Parsing 626/1114 from baseline:pubmed22n0453.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 4.396081924438477\n",
      "Parsing 627/1114 from baseline:pubmed22n0670.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.485511064529419\n",
      "Parsing 628/1114 from baseline:pubmed22n0102.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.549513339996338\n",
      "Parsing 629/1114 from baseline:pubmed22n1007.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.15615701675415\n",
      "Parsing 630/1114 from baseline:pubmed22n0243.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.858163118362427\n",
      "Parsing 631/1114 from baseline:pubmed22n0810.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.044163465499878\n",
      "Parsing 632/1114 from baseline:pubmed22n0696.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.872877359390259\n",
      "Parsing 633/1114 from baseline:pubmed22n0936.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.254588842391968\n",
      "Parsing 634/1114 from baseline:pubmed22n1106.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.182683229446411\n",
      "Parsing 635/1114 from baseline:pubmed22n0177.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.507812976837158\n",
      "Parsing 636/1114 from baseline:pubmed22n1005.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.893491983413696\n",
      "Parsing 637/1114 from baseline:pubmed22n0977.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.744897365570068\n",
      "Parsing 638/1114 from baseline:pubmed22n0836.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.066272974014282\n",
      "Parsing 639/1114 from baseline:pubmed22n0622.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.681101560592651\n",
      "Parsing 640/1114 from baseline:pubmed22n0342.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.511799335479736\n",
      "Parsing 641/1114 from baseline:pubmed22n0890.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.647120237350464\n",
      "Parsing 642/1114 from baseline:pubmed22n0867.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.260164499282837\n",
      "Parsing 643/1114 from baseline:pubmed22n0019.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.550626754760742\n",
      "Parsing 644/1114 from baseline:pubmed22n0710.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.79147744178772\n",
      "Parsing 645/1114 from baseline:pubmed22n0649.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.403099298477173\n",
      "Parsing 646/1114 from baseline:pubmed22n0447.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.411828517913818\n",
      "Parsing 647/1114 from baseline:pubmed22n0998.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.906150579452515\n",
      "Parsing 648/1114 from baseline:pubmed22n0023.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.5634126663208\n",
      "Parsing 649/1114 from baseline:pubmed22n0749.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.725157022476196\n",
      "Parsing 650/1114 from baseline:pubmed22n0822.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.006812572479248\n",
      "Parsing 651/1114 from baseline:pubmed22n0017.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.45024847984314\n",
      "Parsing 652/1114 from baseline:pubmed22n0695.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.25366759300232\n",
      "Parsing 653/1114 from baseline:pubmed22n0642.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.0772705078125\n",
      "Parsing 654/1114 from baseline:pubmed22n0743.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.609786033630371\n",
      "Parsing 655/1114 from baseline:pubmed22n0790.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.562645435333252\n",
      "Parsing 656/1114 from baseline:pubmed22n0088.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.072122812271118\n",
      "Parsing 657/1114 from baseline:pubmed22n0675.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.029757738113403\n",
      "Parsing 658/1114 from baseline:pubmed22n0902.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.945694208145142\n",
      "Parsing 659/1114 from baseline:pubmed22n0926.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.722703456878662\n",
      "Parsing 660/1114 from baseline:pubmed22n0089.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.19921612739563\n",
      "Parsing 661/1114 from baseline:pubmed22n0176.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.144750833511353\n",
      "Parsing 662/1114 from baseline:pubmed22n0716.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.789392709732056\n",
      "Parsing 663/1114 from baseline:pubmed22n1058.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.618969202041626\n",
      "Parsing 664/1114 from baseline:pubmed22n0866.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.944620609283447\n",
      "Parsing 665/1114 from baseline:pubmed22n0375.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.159867286682129\n",
      "Parsing 666/1114 from baseline:pubmed22n0992.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.5159642696380615\n",
      "Parsing 667/1114 from baseline:pubmed22n0655.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.880544900894165\n",
      "Parsing 668/1114 from baseline:pubmed22n0086.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.446832418441772\n",
      "Parsing 669/1114 from baseline:pubmed22n0915.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.925618171691895\n",
      "Parsing 670/1114 from baseline:pubmed22n0402.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.621663570404053\n",
      "Parsing 671/1114 from baseline:pubmed22n0817.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.750831842422485\n",
      "Parsing 672/1114 from baseline:pubmed22n0209.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.864777565002441\n",
      "Parsing 673/1114 from baseline:pubmed22n0609.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.269448518753052\n",
      "Parsing 674/1114 from baseline:pubmed22n0047.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.3343939781188965\n",
      "Parsing 675/1114 from baseline:pubmed22n0438.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.10844898223877\n",
      "Parsing 676/1114 from baseline:pubmed22n0833.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.83797574043274\n",
      "Parsing 677/1114 from baseline:pubmed22n0621.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.084757089614868\n",
      "Parsing 678/1114 from baseline:pubmed22n0115.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.765514373779297\n",
      "Parsing 679/1114 from baseline:pubmed22n0390.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.622238159179688\n",
      "Parsing 680/1114 from baseline:pubmed22n1019.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.921176195144653\n",
      "Parsing 681/1114 from baseline:pubmed22n0887.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.670032978057861\n",
      "Parsing 682/1114 from baseline:pubmed22n0757.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.884046792984009\n",
      "Parsing 683/1114 from baseline:pubmed22n0292.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.49918246269226\n",
      "Parsing 684/1114 from baseline:pubmed22n0882.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.742674350738525\n",
      "Parsing 685/1114 from baseline:pubmed22n0195.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.662231206893921\n",
      "Parsing 686/1114 from baseline:pubmed22n0906.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.489905595779419\n",
      "Parsing 687/1114 from baseline:pubmed22n0385.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.05771279335022\n",
      "Parsing 688/1114 from baseline:pubmed22n0664.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.445056200027466\n",
      "Parsing 689/1114 from baseline:pubmed22n0055.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.15086555480957\n",
      "Parsing 690/1114 from baseline:pubmed22n0487.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.534931421279907\n",
      "Parsing 691/1114 from baseline:pubmed22n0090.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.595798254013062\n",
      "Parsing 692/1114 from baseline:pubmed22n0586.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.0968241691589355\n",
      "Parsing 693/1114 from baseline:pubmed22n0198.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.835066556930542\n",
      "Parsing 694/1114 from baseline:pubmed22n0561.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.402780294418335\n",
      "Parsing 695/1114 from baseline:pubmed22n0217.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.606245040893555\n",
      "Parsing 696/1114 from baseline:pubmed22n0566.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.685669422149658\n",
      "Parsing 697/1114 from baseline:pubmed22n0753.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.547526121139526\n",
      "Parsing 698/1114 from baseline:pubmed22n1024.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.941372156143188\n",
      "Parsing 699/1114 from baseline:pubmed22n0347.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.577543020248413\n",
      "Parsing 700/1114 from baseline:pubmed22n0735.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.429107666015625\n",
      "Parsing 701/1114 from baseline:pubmed22n0730.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.366028547286987\n",
      "Parsing 702/1114 from baseline:pubmed22n0459.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.562565565109253\n",
      "Parsing 703/1114 from baseline:pubmed22n1068.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.580875873565674\n",
      "Parsing 704/1114 from baseline:pubmed22n0099.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.674241781234741\n",
      "Parsing 705/1114 from baseline:pubmed22n0821.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.269054889678955\n",
      "Parsing 706/1114 from baseline:pubmed22n0237.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.636969804763794\n",
      "Parsing 707/1114 from baseline:pubmed22n0302.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.20581841468811\n",
      "Parsing 708/1114 from baseline:pubmed22n0997.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.826698541641235\n",
      "Parsing 709/1114 from baseline:pubmed22n0327.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.769659042358398\n",
      "Parsing 710/1114 from baseline:pubmed22n0398.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.940050840377808\n",
      "Parsing 711/1114 from baseline:pubmed22n0210.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.404935359954834\n",
      "Parsing 712/1114 from baseline:pubmed22n0736.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.54085636138916\n",
      "Parsing 713/1114 from baseline:pubmed22n1026.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.654163837432861\n",
      "Parsing 714/1114 from baseline:pubmed22n0010.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.612991333007812\n",
      "Parsing 715/1114 from baseline:pubmed22n0648.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.488307237625122\n",
      "Parsing 716/1114 from baseline:pubmed22n1037.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.551753759384155\n",
      "Parsing 717/1114 from baseline:pubmed22n0715.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.402381896972656\n",
      "Parsing 718/1114 from baseline:pubmed22n0007.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.237691879272461\n",
      "Parsing 719/1114 from baseline:pubmed22n0589.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.977948188781738\n",
      "Parsing 720/1114 from baseline:pubmed22n1084.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.199337482452393\n",
      "Parsing 721/1114 from baseline:pubmed22n0949.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.169311046600342\n",
      "Parsing 722/1114 from baseline:pubmed22n0082.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.901068925857544\n",
      "Parsing 723/1114 from baseline:pubmed22n0393.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.201663970947266\n",
      "Parsing 724/1114 from baseline:pubmed22n0607.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.276162385940552\n",
      "Parsing 725/1114 from baseline:pubmed22n0384.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.72714376449585\n",
      "Parsing 726/1114 from baseline:pubmed22n0389.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.0367112159729\n",
      "Parsing 727/1114 from baseline:pubmed22n0681.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.14843201637268\n",
      "Parsing 728/1114 from baseline:pubmed22n0073.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.745129346847534\n",
      "Parsing 729/1114 from baseline:pubmed22n0878.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.315313339233398\n",
      "Parsing 730/1114 from baseline:pubmed22n0049.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.496265411376953\n",
      "Parsing 731/1114 from baseline:pubmed22n0113.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.727863311767578\n",
      "Parsing 732/1114 from baseline:pubmed22n0608.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.389576435089111\n",
      "Parsing 733/1114 from baseline:pubmed22n0984.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.322931051254272\n",
      "Parsing 734/1114 from baseline:pubmed22n0083.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.0416841506958\n",
      "Parsing 735/1114 from baseline:pubmed22n0129.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.391896963119507\n",
      "Parsing 736/1114 from baseline:pubmed22n0136.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.354724645614624\n",
      "Parsing 737/1114 from baseline:pubmed22n0103.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.845260381698608\n",
      "Parsing 738/1114 from baseline:pubmed22n1033.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.752774000167847\n",
      "Parsing 739/1114 from baseline:pubmed22n0376.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.142217636108398\n",
      "Parsing 740/1114 from baseline:pubmed22n0401.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.378681659698486\n",
      "Parsing 741/1114 from baseline:pubmed22n0336.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.151980876922607\n",
      "Parsing 742/1114 from baseline:pubmed22n0955.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.899182558059692\n",
      "Parsing 743/1114 from baseline:pubmed22n0804.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.376145362854004\n",
      "Parsing 744/1114 from baseline:pubmed22n0508.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.868865251541138\n",
      "Parsing 745/1114 from baseline:pubmed22n1075.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.143281698226929\n",
      "Parsing 746/1114 from baseline:pubmed22n0263.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.552114248275757\n",
      "Parsing 747/1114 from baseline:pubmed22n0591.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.673445224761963\n",
      "Parsing 748/1114 from baseline:pubmed22n0272.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.26762080192566\n",
      "Parsing 749/1114 from baseline:pubmed22n0335.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.638729095458984\n",
      "Parsing 750/1114 from baseline:pubmed22n0996.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.835742950439453\n",
      "Parsing 751/1114 from baseline:pubmed22n0367.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.520763397216797\n",
      "Parsing 752/1114 from baseline:pubmed22n0034.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.340659141540527\n",
      "Parsing 753/1114 from baseline:pubmed22n0721.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.502104043960571\n",
      "Parsing 754/1114 from baseline:pubmed22n1049.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.022675275802612\n",
      "Parsing 755/1114 from baseline:pubmed22n0322.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.676187753677368\n",
      "Parsing 756/1114 from baseline:pubmed22n0601.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.347476720809937\n",
      "Parsing 757/1114 from baseline:pubmed22n0282.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.651323795318604\n",
      "Parsing 758/1114 from baseline:pubmed22n0370.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.021174907684326\n",
      "Parsing 759/1114 from baseline:pubmed22n0741.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.588047504425049\n",
      "Parsing 760/1114 from baseline:pubmed22n0580.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.740442514419556\n",
      "Parsing 761/1114 from baseline:pubmed22n0944.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.628875970840454\n",
      "Parsing 762/1114 from baseline:pubmed22n0180.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.116307973861694\n",
      "Parsing 763/1114 from baseline:pubmed22n0717.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 5.995166540145874\n",
      "Parsing 764/1114 from baseline:pubmed22n0485.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.77578616142273\n",
      "Parsing 765/1114 from baseline:pubmed22n1085.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.538527250289917\n",
      "Parsing 766/1114 from baseline:pubmed22n0706.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 5.823636770248413\n",
      "Parsing 767/1114 from baseline:pubmed22n0331.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.929679155349731\n",
      "Parsing 768/1114 from baseline:pubmed22n0498.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.609055757522583\n",
      "Parsing 769/1114 from baseline:pubmed22n0404.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.998200178146362\n",
      "Parsing 770/1114 from baseline:pubmed22n0291.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.843368768692017\n",
      "Parsing 771/1114 from baseline:pubmed22n0911.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.483885288238525\n",
      "Parsing 772/1114 from baseline:pubmed22n0789.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 13.142366647720337\n",
      "Parsing 773/1114 from baseline:pubmed22n1087.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.245652914047241\n",
      "Parsing 774/1114 from baseline:pubmed22n0713.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.065542221069336\n",
      "Parsing 775/1114 from baseline:pubmed22n0481.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.383139371871948\n",
      "Parsing 776/1114 from baseline:pubmed22n1090.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.272372484207153\n",
      "Parsing 777/1114 from baseline:pubmed22n0160.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.990597248077393\n",
      "Parsing 778/1114 from baseline:pubmed22n0636.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.503901720046997\n",
      "Parsing 779/1114 from baseline:pubmed22n1056.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.711517095565796\n",
      "Parsing 780/1114 from baseline:pubmed22n0861.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.434305429458618\n",
      "Parsing 781/1114 from baseline:pubmed22n0455.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.432782411575317\n",
      "Parsing 782/1114 from baseline:pubmed22n0445.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.31973648071289\n",
      "Parsing 783/1114 from baseline:pubmed22n0518.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.964443445205688\n",
      "Parsing 784/1114 from baseline:pubmed22n0295.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.777976512908936\n",
      "Parsing 785/1114 from baseline:pubmed22n0396.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.040231943130493\n",
      "Parsing 786/1114 from baseline:pubmed22n0844.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.965678215026855\n",
      "Parsing 787/1114 from baseline:pubmed22n1053.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.364557981491089\n",
      "Parsing 788/1114 from baseline:pubmed22n0545.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.418394565582275\n",
      "Parsing 789/1114 from baseline:pubmed22n1098.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.94135308265686\n",
      "Parsing 790/1114 from baseline:pubmed22n0399.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.13060188293457\n",
      "Parsing 791/1114 from baseline:pubmed22n0840.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.825718402862549\n",
      "Parsing 792/1114 from baseline:pubmed22n0797.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.922139644622803\n",
      "Parsing 793/1114 from baseline:pubmed22n0981.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.846426486968994\n",
      "Parsing 794/1114 from baseline:pubmed22n0356.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.770131826400757\n",
      "Parsing 795/1114 from baseline:pubmed22n0079.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.5350775718688965\n",
      "Parsing 796/1114 from baseline:pubmed22n0190.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.886589527130127\n",
      "Parsing 797/1114 from baseline:pubmed22n0378.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.029411315917969\n",
      "Parsing 798/1114 from baseline:pubmed22n0807.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.962253093719482\n",
      "Parsing 799/1114 from baseline:pubmed22n0068.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.452553272247314\n",
      "Parsing 800/1114 from baseline:pubmed22n0147.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.26113486289978\n",
      "Parsing 801/1114 from baseline:pubmed22n0921.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.51865005493164\n",
      "Parsing 802/1114 from baseline:pubmed22n0744.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.192288637161255\n",
      "Parsing 803/1114 from baseline:pubmed22n0514.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.041338205337524\n",
      "Parsing 804/1114 from baseline:pubmed22n0819.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.99436068534851\n",
      "Parsing 805/1114 from baseline:pubmed22n0620.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.350825309753418\n",
      "Parsing 806/1114 from baseline:pubmed22n0026.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.429303169250488\n",
      "Parsing 807/1114 from baseline:pubmed22n0752.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.990627765655518\n",
      "Parsing 808/1114 from baseline:pubmed22n0354.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.914018392562866\n",
      "Parsing 809/1114 from baseline:pubmed22n0811.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.342264413833618\n",
      "Parsing 810/1114 from baseline:pubmed22n0119.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.433761358261108\n",
      "Parsing 811/1114 from baseline:pubmed22n0037.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.143345832824707\n",
      "Parsing 812/1114 from baseline:pubmed22n0246.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.743114948272705\n",
      "Parsing 813/1114 from baseline:pubmed22n1025.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.038145780563354\n",
      "Parsing 814/1114 from baseline:pubmed22n0972.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.69667935371399\n",
      "Parsing 815/1114 from baseline:pubmed22n0366.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.368228197097778\n",
      "Parsing 816/1114 from baseline:pubmed22n0161.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.679102182388306\n",
      "Parsing 817/1114 from baseline:pubmed22n0793.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.537821531295776\n",
      "Parsing 818/1114 from baseline:pubmed22n0091.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.707046031951904\n",
      "Parsing 819/1114 from baseline:pubmed22n0860.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.816159963607788\n",
      "Parsing 820/1114 from baseline:pubmed22n0958.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.051103591918945\n",
      "Parsing 821/1114 from baseline:pubmed22n1094.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.190733909606934\n",
      "Parsing 822/1114 from baseline:pubmed22n0250.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.676402807235718\n",
      "Parsing 823/1114 from baseline:pubmed22n0298.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.639510154724121\n",
      "Parsing 824/1114 from baseline:pubmed22n0273.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.396833896636963\n",
      "Parsing 825/1114 from baseline:pubmed22n0057.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.564096689224243\n",
      "Parsing 826/1114 from baseline:pubmed22n0703.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.840831756591797\n",
      "Parsing 827/1114 from baseline:pubmed22n0897.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.997662544250488\n",
      "Parsing 828/1114 from baseline:pubmed22n0412.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.681427955627441\n",
      "Parsing 829/1114 from baseline:pubmed22n0193.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.264249324798584\n",
      "Parsing 830/1114 from baseline:pubmed22n0868.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.128715515136719\n",
      "Parsing 831/1114 from baseline:pubmed22n0204.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.797265768051147\n",
      "Parsing 832/1114 from baseline:pubmed22n0763.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.310788869857788\n",
      "Parsing 833/1114 from baseline:pubmed22n0066.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.743533372879028\n",
      "Parsing 834/1114 from baseline:pubmed22n0364.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.497556686401367\n",
      "Parsing 835/1114 from baseline:pubmed22n0551.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.038954019546509\n",
      "Parsing 836/1114 from baseline:pubmed22n0830.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.823853492736816\n",
      "Parsing 837/1114 from baseline:pubmed22n0182.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.695734739303589\n",
      "Parsing 838/1114 from baseline:pubmed22n0560.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.909664869308472\n",
      "Parsing 839/1114 from baseline:pubmed22n0786.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.355292558670044\n",
      "Parsing 840/1114 from baseline:pubmed22n0200.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.169004917144775\n",
      "Parsing 841/1114 from baseline:pubmed22n0056.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.932010650634766\n",
      "Parsing 842/1114 from baseline:pubmed22n0553.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.410529613494873\n",
      "Parsing 843/1114 from baseline:pubmed22n0429.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.664073944091797\n",
      "Parsing 844/1114 from baseline:pubmed22n0308.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.064719438552856\n",
      "Parsing 845/1114 from baseline:pubmed22n0507.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.802934408187866\n",
      "Parsing 846/1114 from baseline:pubmed22n0202.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.025578022003174\n",
      "Parsing 847/1114 from baseline:pubmed22n0172.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.338615417480469\n",
      "Parsing 848/1114 from baseline:pubmed22n0726.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.331538438796997\n",
      "Parsing 849/1114 from baseline:pubmed22n0444.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.055877685546875\n",
      "Parsing 850/1114 from baseline:pubmed22n0373.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.361202955245972\n",
      "Parsing 851/1114 from baseline:pubmed22n0450.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.172860383987427\n",
      "Parsing 852/1114 from baseline:pubmed22n0791.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.480916738510132\n",
      "Parsing 853/1114 from baseline:pubmed22n0087.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.21137022972107\n",
      "Parsing 854/1114 from baseline:pubmed22n0557.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.59911823272705\n",
      "Parsing 855/1114 from baseline:pubmed22n0280.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.832123756408691\n",
      "Parsing 856/1114 from baseline:pubmed22n0747.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.937412738800049\n",
      "Parsing 857/1114 from baseline:pubmed22n0325.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.106613159179688\n",
      "Parsing 858/1114 from baseline:pubmed22n0572.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.039812326431274\n",
      "Parsing 859/1114 from baseline:pubmed22n1095.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.495657205581665\n",
      "Parsing 860/1114 from baseline:pubmed22n0683.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.098406553268433\n",
      "Parsing 861/1114 from baseline:pubmed22n0966.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.95550537109375\n",
      "Parsing 862/1114 from baseline:pubmed22n0823.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.364991188049316\n",
      "Parsing 863/1114 from baseline:pubmed22n0443.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.448652982711792\n",
      "Parsing 864/1114 from baseline:pubmed22n0486.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.215084791183472\n",
      "Parsing 865/1114 from baseline:pubmed22n0521.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.459978342056274\n",
      "Parsing 866/1114 from baseline:pubmed22n0773.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.66658639907837\n",
      "Parsing 867/1114 from baseline:pubmed22n1000.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.871379613876343\n",
      "Parsing 868/1114 from baseline:pubmed22n0971.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.905842065811157\n",
      "Parsing 869/1114 from baseline:pubmed22n0640.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.005221366882324\n",
      "Parsing 870/1114 from baseline:pubmed22n0857.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 13.073050022125244\n",
      "Parsing 871/1114 from baseline:pubmed22n1082.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.868976354598999\n",
      "Parsing 872/1114 from baseline:pubmed22n1061.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.117353916168213\n",
      "Parsing 873/1114 from baseline:pubmed22n0976.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.519693851470947\n",
      "Parsing 874/1114 from baseline:pubmed22n0893.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.96321702003479\n",
      "Parsing 875/1114 from baseline:pubmed22n0975.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.905799627304077\n",
      "Parsing 876/1114 from baseline:pubmed22n0196.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.056237697601318\n",
      "Parsing 877/1114 from baseline:pubmed22n0659.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.57107424736023\n",
      "Parsing 878/1114 from baseline:pubmed22n0630.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.294666528701782\n",
      "Parsing 879/1114 from baseline:pubmed22n0993.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.933852195739746\n",
      "Parsing 880/1114 from baseline:pubmed22n0062.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.647849798202515\n",
      "Parsing 881/1114 from baseline:pubmed22n0268.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.918034553527832\n",
      "Parsing 882/1114 from baseline:pubmed22n1020.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.43210220336914\n",
      "Parsing 883/1114 from baseline:pubmed22n0734.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.685798645019531\n",
      "Parsing 884/1114 from baseline:pubmed22n0020.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.931552171707153\n",
      "Parsing 885/1114 from baseline:pubmed22n0627.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.041439533233643\n",
      "Parsing 886/1114 from baseline:pubmed22n0587.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.603755474090576\n",
      "Parsing 887/1114 from baseline:pubmed22n1044.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.920992851257324\n",
      "Parsing 888/1114 from baseline:pubmed22n0372.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.64613151550293\n",
      "Parsing 889/1114 from baseline:pubmed22n1011.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.398974180221558\n",
      "Parsing 890/1114 from baseline:pubmed22n0458.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.874047994613647\n",
      "Parsing 891/1114 from baseline:pubmed22n0142.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.881676435470581\n",
      "Parsing 892/1114 from baseline:pubmed22n0907.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.664865016937256\n",
      "Parsing 893/1114 from baseline:pubmed22n0265.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.975796937942505\n",
      "Parsing 894/1114 from baseline:pubmed22n0351.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.185555219650269\n",
      "Parsing 895/1114 from baseline:pubmed22n0050.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.894487142562866\n",
      "Parsing 896/1114 from baseline:pubmed22n0311.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.657239437103271\n",
      "Parsing 897/1114 from baseline:pubmed22n0983.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.926023244857788\n",
      "Parsing 898/1114 from baseline:pubmed22n0350.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.918477296829224\n",
      "Parsing 899/1114 from baseline:pubmed22n0953.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.807024478912354\n",
      "Parsing 900/1114 from baseline:pubmed22n0225.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.317901611328125\n",
      "Parsing 901/1114 from baseline:pubmed22n0956.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.914797067642212\n",
      "Parsing 902/1114 from baseline:pubmed22n0865.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.498563528060913\n",
      "Parsing 903/1114 from baseline:pubmed22n0884.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.0448527336120605\n",
      "Parsing 904/1114 from baseline:pubmed22n0503.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.87693452835083\n",
      "Parsing 905/1114 from baseline:pubmed22n1064.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.123239994049072\n",
      "Parsing 906/1114 from baseline:pubmed22n0315.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.783531188964844\n",
      "Parsing 907/1114 from baseline:pubmed22n0759.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.669766426086426\n",
      "Parsing 908/1114 from baseline:pubmed22n0588.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.450839519500732\n",
      "Parsing 909/1114 from baseline:pubmed22n0714.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.224055290222168\n",
      "Parsing 910/1114 from baseline:pubmed22n0702.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.777575492858887\n",
      "Parsing 911/1114 from baseline:pubmed22n0870.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.16417121887207\n",
      "Parsing 912/1114 from baseline:pubmed22n0916.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.650100946426392\n",
      "Parsing 913/1114 from baseline:pubmed22n0829.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.280519008636475\n",
      "Parsing 914/1114 from baseline:pubmed22n1069.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.813172101974487\n",
      "Parsing 915/1114 from baseline:pubmed22n0344.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.518751859664917\n",
      "Parsing 916/1114 from baseline:pubmed22n0827.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.88667368888855\n",
      "Parsing 917/1114 from baseline:pubmed22n0146.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.402334213256836\n",
      "Parsing 918/1114 from baseline:pubmed22n0436.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.585164308547974\n",
      "Parsing 919/1114 from baseline:pubmed22n0462.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.380978345870972\n",
      "Parsing 920/1114 from baseline:pubmed22n0235.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.048476934432983\n",
      "Parsing 921/1114 from baseline:pubmed22n0141.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.147132396697998\n",
      "Parsing 922/1114 from baseline:pubmed22n0065.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.944382429122925\n",
      "Parsing 923/1114 from baseline:pubmed22n0381.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.31889295578003\n",
      "Parsing 924/1114 from baseline:pubmed22n0120.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.521684646606445\n",
      "Parsing 925/1114 from baseline:pubmed22n0552.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.863131999969482\n",
      "Parsing 926/1114 from baseline:pubmed22n0117.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.48314905166626\n",
      "Parsing 927/1114 from baseline:pubmed22n0610.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.765660524368286\n",
      "Parsing 928/1114 from baseline:pubmed22n0796.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.68809962272644\n",
      "Parsing 929/1114 from baseline:pubmed22n1112.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.914399147033691\n",
      "Parsing 930/1114 from baseline:pubmed22n0025.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.49167275428772\n",
      "Parsing 931/1114 from baseline:pubmed22n0341.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.51409912109375\n",
      "Parsing 932/1114 from baseline:pubmed22n0754.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.442100048065186\n",
      "Parsing 933/1114 from baseline:pubmed22n0281.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.455981969833374\n",
      "Parsing 934/1114 from baseline:pubmed22n0388.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.10144305229187\n",
      "Parsing 935/1114 from baseline:pubmed22n0677.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.915344476699829\n",
      "Parsing 936/1114 from baseline:pubmed22n0493.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.542317867279053\n",
      "Parsing 937/1114 from baseline:pubmed22n0935.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.592689752578735\n",
      "Parsing 938/1114 from baseline:pubmed22n0365.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.45843505859375\n",
      "Parsing 939/1114 from baseline:pubmed22n0186.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.562849521636963\n",
      "Parsing 940/1114 from baseline:pubmed22n1045.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.040143013000488\n",
      "Parsing 941/1114 from baseline:pubmed22n0423.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.636410474777222\n",
      "Parsing 942/1114 from baseline:pubmed22n0095.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.962398767471313\n",
      "Parsing 943/1114 from baseline:pubmed22n0919.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.01618242263794\n",
      "Parsing 944/1114 from baseline:pubmed22n0528.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.94079327583313\n",
      "Parsing 945/1114 from baseline:pubmed22n0046.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.58482551574707\n",
      "Parsing 946/1114 from baseline:pubmed22n0876.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.520980596542358\n",
      "Parsing 947/1114 from baseline:pubmed22n0616.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.522033929824829\n",
      "Parsing 948/1114 from baseline:pubmed22n0854.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.658381938934326\n",
      "Parsing 949/1114 from baseline:pubmed22n0206.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.178976058959961\n",
      "Parsing 950/1114 from baseline:pubmed22n0723.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.08882761001587\n",
      "Parsing 951/1114 from baseline:pubmed22n0369.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.212918043136597\n",
      "Parsing 952/1114 from baseline:pubmed22n0934.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.731549978256226\n",
      "Parsing 953/1114 from baseline:pubmed22n0764.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.02899956703186\n",
      "Parsing 954/1114 from baseline:pubmed22n0197.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.303652286529541\n",
      "Parsing 955/1114 from baseline:pubmed22n0699.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.140287160873413\n",
      "Parsing 956/1114 from baseline:pubmed22n0240.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.896121501922607\n",
      "Parsing 957/1114 from baseline:pubmed22n0788.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.452723741531372\n",
      "Parsing 958/1114 from baseline:pubmed22n0707.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.6921968460083\n",
      "Parsing 959/1114 from baseline:pubmed22n0598.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.554663896560669\n",
      "Parsing 960/1114 from baseline:pubmed22n0582.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.861047267913818\n",
      "Parsing 961/1114 from baseline:pubmed22n0662.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.654750347137451\n",
      "Parsing 962/1114 from baseline:pubmed22n0152.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.507732629776001\n",
      "Parsing 963/1114 from baseline:pubmed22n0965.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.557297706604004\n",
      "Parsing 964/1114 from baseline:pubmed22n0581.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.299372673034668\n",
      "Parsing 965/1114 from baseline:pubmed22n0728.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.618117809295654\n",
      "Parsing 966/1114 from baseline:pubmed22n0806.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.013031244277954\n",
      "Parsing 967/1114 from baseline:pubmed22n0912.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.775091886520386\n",
      "Parsing 968/1114 from baseline:pubmed22n0724.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.87713360786438\n",
      "Parsing 969/1114 from baseline:pubmed22n0939.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.594416856765747\n",
      "Parsing 970/1114 from baseline:pubmed22n0174.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.187556982040405\n",
      "Parsing 971/1114 from baseline:pubmed22n0646.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.238092184066772\n",
      "Parsing 972/1114 from baseline:pubmed22n0700.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.689152002334595\n",
      "Parsing 973/1114 from baseline:pubmed22n1014.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.203443050384521\n",
      "Parsing 974/1114 from baseline:pubmed22n0883.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.968036890029907\n",
      "Parsing 975/1114 from baseline:pubmed22n0053.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.333784103393555\n",
      "Parsing 976/1114 from baseline:pubmed22n0104.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.16835331916809\n",
      "Parsing 977/1114 from baseline:pubmed22n0502.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.731077194213867\n",
      "Parsing 978/1114 from baseline:pubmed22n0264.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.523353099822998\n",
      "Parsing 979/1114 from baseline:pubmed22n0154.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.876108169555664\n",
      "Parsing 980/1114 from baseline:pubmed22n0947.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.796398878097534\n",
      "Parsing 981/1114 from baseline:pubmed22n0781.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.146822690963745\n",
      "Parsing 982/1114 from baseline:pubmed22n0001.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.947500228881836\n",
      "Parsing 983/1114 from baseline:pubmed22n0081.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.50605034828186\n",
      "Parsing 984/1114 from baseline:pubmed22n0275.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.330862998962402\n",
      "Parsing 985/1114 from baseline:pubmed22n0661.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.986053228378296\n",
      "Parsing 986/1114 from baseline:pubmed22n0492.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.890100717544556\n",
      "Parsing 987/1114 from baseline:pubmed22n0207.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.78211522102356\n",
      "Parsing 988/1114 from baseline:pubmed22n1088.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.274892807006836\n",
      "Parsing 989/1114 from baseline:pubmed22n0430.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.391764640808105\n",
      "Parsing 990/1114 from baseline:pubmed22n0742.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.74393630027771\n",
      "Parsing 991/1114 from baseline:pubmed22n0548.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.90346097946167\n",
      "Parsing 992/1114 from baseline:pubmed22n0171.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.859782218933105\n",
      "Parsing 993/1114 from baseline:pubmed22n1074.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.712568283081055\n",
      "Parsing 994/1114 from baseline:pubmed22n0688.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.343299388885498\n",
      "Parsing 995/1114 from baseline:pubmed22n0096.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.647935628890991\n",
      "Parsing 996/1114 from baseline:pubmed22n0144.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.077581644058228\n",
      "Parsing 997/1114 from baseline:pubmed22n0058.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 5.883482456207275\n",
      "Parsing 998/1114 from baseline:pubmed22n0654.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.170053482055664\n",
      "Parsing 999/1114 from baseline:pubmed22n0512.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.582052707672119\n",
      "Parsing 1000/1114 from baseline:pubmed22n0183.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.117900371551514\n",
      "Parsing 1001/1114 from baseline:pubmed22n0169.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.792304515838623\n",
      "Parsing 1002/1114 from baseline:pubmed22n0803.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.986154317855835\n",
      "Parsing 1003/1114 from baseline:pubmed22n0211.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.783765316009521\n",
      "Parsing 1004/1114 from baseline:pubmed22n0143.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.98093867301941\n",
      "Parsing 1005/1114 from baseline:pubmed22n0054.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.954633474349976\n",
      "Parsing 1006/1114 from baseline:pubmed22n0326.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.364425897598267\n",
      "Parsing 1007/1114 from baseline:pubmed22n0574.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.123034000396729\n",
      "Parsing 1008/1114 from baseline:pubmed22n0491.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.972645998001099\n",
      "Parsing 1009/1114 from baseline:pubmed22n0698.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.491865873336792\n",
      "Parsing 1010/1114 from baseline:pubmed22n0571.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.93613052368164\n",
      "Parsing 1011/1114 from baseline:pubmed22n0962.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.674167633056641\n",
      "Parsing 1012/1114 from baseline:pubmed22n0230.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.453224897384644\n",
      "Parsing 1013/1114 from baseline:pubmed22n1052.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.215310335159302\n",
      "Parsing 1014/1114 from baseline:pubmed22n1047.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.089988946914673\n",
      "Parsing 1015/1114 from baseline:pubmed22n0408.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.123547315597534\n",
      "Parsing 1016/1114 from baseline:pubmed22n0244.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.136234998703003\n",
      "Parsing 1017/1114 from baseline:pubmed22n0490.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.18812084197998\n",
      "Parsing 1018/1114 from baseline:pubmed22n0329.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.249976873397827\n",
      "Parsing 1019/1114 from baseline:pubmed22n0427.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.198402404785156\n",
      "Parsing 1020/1114 from baseline:pubmed22n0151.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.409255027770996\n",
      "Parsing 1021/1114 from baseline:pubmed22n0044.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.084430694580078\n",
      "Parsing 1022/1114 from baseline:pubmed22n0813.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.152750492095947\n",
      "Parsing 1023/1114 from baseline:pubmed22n0701.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.064077854156494\n",
      "Parsing 1024/1114 from baseline:pubmed22n0873.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.47325873374939\n",
      "Parsing 1025/1114 from baseline:pubmed22n1083.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.360184669494629\n",
      "Parsing 1026/1114 from baseline:pubmed22n0256.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.95722770690918\n",
      "Parsing 1027/1114 from baseline:pubmed22n0409.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.966776609420776\n",
      "Parsing 1028/1114 from baseline:pubmed22n0950.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.226748943328857\n",
      "Parsing 1029/1114 from baseline:pubmed22n0339.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 5.730759382247925\n",
      "Parsing 1030/1114 from baseline:pubmed22n0577.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.277870416641235\n",
      "Parsing 1031/1114 from baseline:pubmed22n0371.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.912600517272949\n",
      "Parsing 1032/1114 from baseline:pubmed22n0009.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.695233583450317\n",
      "Parsing 1033/1114 from baseline:pubmed22n0092.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.351094722747803\n",
      "Parsing 1034/1114 from baseline:pubmed22n0013.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.369818449020386\n",
      "Parsing 1035/1114 from baseline:pubmed22n0157.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.056817531585693\n",
      "Parsing 1036/1114 from baseline:pubmed22n0139.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.048660516738892\n",
      "Parsing 1037/1114 from baseline:pubmed22n0043.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.127297639846802\n",
      "Parsing 1038/1114 from baseline:pubmed22n0203.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.46862530708313\n",
      "Parsing 1039/1114 from baseline:pubmed22n1113.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.138504981994629\n",
      "Parsing 1040/1114 from baseline:pubmed22n0859.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.197927951812744\n",
      "Parsing 1041/1114 from baseline:pubmed22n0576.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.500072479248047\n",
      "Parsing 1042/1114 from baseline:pubmed22n0631.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.192078351974487\n",
      "Parsing 1043/1114 from baseline:pubmed22n0511.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.172670602798462\n",
      "Parsing 1044/1114 from baseline:pubmed22n0671.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.869782209396362\n",
      "Parsing 1045/1114 from baseline:pubmed22n0149.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.303449630737305\n",
      "Parsing 1046/1114 from baseline:pubmed22n0287.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.463442087173462\n",
      "Parsing 1047/1114 from baseline:pubmed22n0930.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.15593695640564\n",
      "Parsing 1048/1114 from baseline:pubmed22n0679.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.987884998321533\n",
      "Parsing 1049/1114 from baseline:pubmed22n0651.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.978099822998047\n",
      "Parsing 1050/1114 from baseline:pubmed22n0418.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.972163438796997\n",
      "Parsing 1051/1114 from baseline:pubmed22n0845.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.934014081954956\n",
      "Parsing 1052/1114 from baseline:pubmed22n0722.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.207695245742798\n",
      "Parsing 1053/1114 from baseline:pubmed22n0241.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.768735647201538\n",
      "Parsing 1054/1114 from baseline:pubmed22n0831.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.540204048156738\n",
      "Parsing 1055/1114 from baseline:pubmed22n0922.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.224820613861084\n",
      "Parsing 1056/1114 from baseline:pubmed22n0745.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.276444435119629\n",
      "Parsing 1057/1114 from baseline:pubmed22n0748.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.743108987808228\n",
      "Parsing 1058/1114 from baseline:pubmed22n0929.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.060716152191162\n",
      "Parsing 1059/1114 from baseline:pubmed22n0247.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.156614542007446\n",
      "Parsing 1060/1114 from baseline:pubmed22n0288.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.304347038269043\n",
      "Parsing 1061/1114 from baseline:pubmed22n0738.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.122299671173096\n",
      "Parsing 1062/1114 from baseline:pubmed22n0340.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.865911722183228\n",
      "Parsing 1063/1114 from baseline:pubmed22n0094.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.585924863815308\n",
      "Parsing 1064/1114 from baseline:pubmed22n0778.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.8988676071167\n",
      "Parsing 1065/1114 from baseline:pubmed22n0632.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.136444807052612\n",
      "Parsing 1066/1114 from baseline:pubmed22n0242.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.865537166595459\n",
      "Parsing 1067/1114 from baseline:pubmed22n0231.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.046100378036499\n",
      "Parsing 1068/1114 from baseline:pubmed22n0310.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.182926177978516\n",
      "Parsing 1069/1114 from baseline:pubmed22n0426.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.95630669593811\n",
      "Parsing 1070/1114 from baseline:pubmed22n0864.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.692975044250488\n",
      "Parsing 1071/1114 from baseline:pubmed22n0785.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.370311260223389\n",
      "Parsing 1072/1114 from baseline:pubmed22n1039.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.646292448043823\n",
      "Parsing 1073/1114 from baseline:pubmed22n0464.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.250810384750366\n",
      "Parsing 1074/1114 from baseline:pubmed22n0279.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.374626398086548\n",
      "Parsing 1075/1114 from baseline:pubmed22n0014.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.881245374679565\n",
      "Parsing 1076/1114 from baseline:pubmed22n0030.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.301933765411377\n",
      "Parsing 1077/1114 from baseline:pubmed22n0519.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.814806938171387\n",
      "Parsing 1078/1114 from baseline:pubmed22n0213.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.703256607055664\n",
      "Parsing 1079/1114 from baseline:pubmed22n0253.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.34755802154541\n",
      "Parsing 1080/1114 from baseline:pubmed22n0394.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.464753866195679\n",
      "Parsing 1081/1114 from baseline:pubmed22n0175.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.272921085357666\n",
      "Parsing 1082/1114 from baseline:pubmed22n0036.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.47885799407959\n",
      "Parsing 1083/1114 from baseline:pubmed22n0596.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.442493915557861\n",
      "Parsing 1084/1114 from baseline:pubmed22n0594.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.751627206802368\n",
      "Parsing 1085/1114 from baseline:pubmed22n0925.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.000219583511353\n",
      "Parsing 1086/1114 from baseline:pubmed22n0185.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.298893451690674\n",
      "Parsing 1087/1114 from baseline:pubmed22n0111.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.790472507476807\n",
      "Parsing 1088/1114 from baseline:pubmed22n1086.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.780491590499878\n",
      "Parsing 1089/1114 from baseline:pubmed22n0784.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.310731887817383\n",
      "Parsing 1090/1114 from baseline:pubmed22n1067.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.802008628845215\n",
      "Parsing 1091/1114 from baseline:pubmed22n0824.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.816689252853394\n",
      "Parsing 1092/1114 from baseline:pubmed22n1073.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.325598239898682\n",
      "Parsing 1093/1114 from baseline:pubmed22n0704.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.889885187149048\n",
      "Parsing 1094/1114 from baseline:pubmed22n0286.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.357102870941162\n",
      "Parsing 1095/1114 from baseline:pubmed22n0123.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.199187278747559\n",
      "Parsing 1096/1114 from baseline:pubmed22n0943.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.901180028915405\n",
      "Parsing 1097/1114 from baseline:pubmed22n0841.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.009671926498413\n",
      "Parsing 1098/1114 from baseline:pubmed22n0940.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.51240587234497\n",
      "Parsing 1099/1114 from baseline:pubmed22n1013.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.713128566741943\n",
      "Parsing 1100/1114 from baseline:pubmed22n0297.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.74455976486206\n",
      "Parsing 1101/1114 from baseline:pubmed22n0358.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.4746572971344\n",
      "Parsing 1102/1114 from baseline:pubmed22n0756.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.451858282089233\n",
      "Parsing 1103/1114 from baseline:pubmed22n0266.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.033226013183594\n",
      "Parsing 1104/1114 from baseline:pubmed22n0421.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.613743543624878\n",
      "Parsing 1105/1114 from baseline:pubmed22n0301.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.917767763137817\n",
      "Parsing 1106/1114 from baseline:pubmed22n0059.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 6.05495023727417\n",
      "Parsing 1107/1114 from baseline:pubmed22n0484.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.840168476104736\n",
      "Parsing 1108/1114 from baseline:pubmed22n0410.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 7.047401666641235\n",
      "Parsing 1109/1114 from baseline:pubmed22n0035.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.76785945892334\n",
      "Parsing 1110/1114 from baseline:pubmed22n0317.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.986364603042603\n",
      "Parsing 1111/1114 from baseline:pubmed22n0892.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.690650939941406\n",
      "Parsing 1112/1114 from baseline:pubmed22n0914.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 8.561165809631348\n",
      "Parsing 1113/1114 from baseline:pubmed22n0110.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.256555318832397\n",
      "Parsing 1114/1114 from baseline:pubmed22n0590.xml\n",
      "Parsing updatefiles containing 314 bulk files\n",
      "==================================================\n",
      "Parsing finished. 20155 articles parsed.Total time: 7.083954811096191\n",
      "Parsing 1/314 from updatefiles:pubmed22n1364.xml\n",
      "Parsing finished. 16368 articles parsed.Total time: 4.802070379257202\n",
      "Parsing 2/314 from updatefiles:pubmed22n1195.xml\n",
      "Parsing finished. 18747 articles parsed.Total time: 7.619186162948608\n",
      "Parsing 3/314 from updatefiles:pubmed22n1134.xml\n",
      "Parsing finished. 3981 articles parsed.Total time: 1.2645361423492432\n",
      "Parsing 4/314 from updatefiles:pubmed22n1145.xml\n",
      "Parsing finished. 26230 articles parsed.Total time: 9.56923222541809\n",
      "Parsing 5/314 from updatefiles:pubmed22n1301.xml\n",
      "Parsing finished. 7931 articles parsed.Total time: 2.849309206008911\n",
      "Parsing 6/314 from updatefiles:pubmed22n1319.xml\n",
      "Parsing finished. 20345 articles parsed.Total time: 7.448730945587158\n",
      "Parsing 7/314 from updatefiles:pubmed22n1422.xml\n",
      "Parsing finished. 24686 articles parsed.Total time: 9.580057621002197\n",
      "Parsing 8/314 from updatefiles:pubmed22n1126.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.288885354995728\n",
      "Parsing 9/314 from updatefiles:pubmed22n1117.xml\n",
      "Parsing finished. 17672 articles parsed.Total time: 6.095547437667847\n",
      "Parsing 10/314 from updatefiles:pubmed22n1334.xml\n",
      "Parsing finished. 11644 articles parsed.Total time: 4.038263559341431\n",
      "Parsing 11/314 from updatefiles:pubmed22n1264.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.65898060798645\n",
      "Parsing 12/314 from updatefiles:pubmed22n1338.xml\n",
      "Parsing finished. 5048 articles parsed.Total time: 1.6763646602630615\n",
      "Parsing 13/314 from updatefiles:pubmed22n1353.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 15.562711000442505\n",
      "Parsing 14/314 from updatefiles:pubmed22n1390.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.509835481643677\n",
      "Parsing 15/314 from updatefiles:pubmed22n1254.xml\n",
      "Parsing finished. 6938 articles parsed.Total time: 2.204627752304077\n",
      "Parsing 16/314 from updatefiles:pubmed22n1197.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.903393030166626\n",
      "Parsing 17/314 from updatefiles:pubmed22n1344.xml\n",
      "Parsing finished. 19489 articles parsed.Total time: 7.638021469116211\n",
      "Parsing 18/314 from updatefiles:pubmed22n1299.xml\n",
      "Parsing finished. 341 articles parsed.Total time: 0.08800077438354492\n",
      "Parsing 19/314 from updatefiles:pubmed22n1345.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.381487846374512\n",
      "Parsing 20/314 from updatefiles:pubmed22n1163.xml\n",
      "Parsing finished. 24570 articles parsed.Total time: 9.766067028045654\n",
      "Parsing 21/314 from updatefiles:pubmed22n1409.xml\n",
      "Parsing finished. 16621 articles parsed.Total time: 5.443072557449341\n",
      "Parsing 22/314 from updatefiles:pubmed22n1255.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.148256063461304\n",
      "Parsing 23/314 from updatefiles:pubmed22n1293.xml\n",
      "Parsing finished. 952 articles parsed.Total time: 0.37824392318725586\n",
      "Parsing 24/314 from updatefiles:pubmed22n1397.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.49093246459961\n",
      "Parsing 25/314 from updatefiles:pubmed22n1320.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 14.075923681259155\n",
      "Parsing 26/314 from updatefiles:pubmed22n1199.xml\n",
      "Parsing finished. 19166 articles parsed.Total time: 6.006189823150635\n",
      "Parsing 27/314 from updatefiles:pubmed22n1185.xml\n",
      "Parsing finished. 22878 articles parsed.Total time: 8.629982948303223\n",
      "Parsing 28/314 from updatefiles:pubmed22n1150.xml\n",
      "Parsing finished. 20147 articles parsed.Total time: 7.176434278488159\n",
      "Parsing 29/314 from updatefiles:pubmed22n1362.xml\n",
      "Parsing finished. 1429 articles parsed.Total time: 0.464414119720459\n",
      "Parsing 30/314 from updatefiles:pubmed22n1182.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.840512752532959\n",
      "Parsing 31/314 from updatefiles:pubmed22n1394.xml\n",
      "Parsing finished. 23900 articles parsed.Total time: 7.386869668960571\n",
      "Parsing 32/314 from updatefiles:pubmed22n1382.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 16.910902500152588\n",
      "Parsing 33/314 from updatefiles:pubmed22n1174.xml\n",
      "Parsing finished. 3806 articles parsed.Total time: 0.9807589054107666\n",
      "Parsing 34/314 from updatefiles:pubmed22n1292.xml\n",
      "Parsing finished. 22233 articles parsed.Total time: 8.284057140350342\n",
      "Parsing 35/314 from updatefiles:pubmed22n1279.xml\n",
      "Parsing finished. 23549 articles parsed.Total time: 8.941875696182251\n",
      "Parsing 36/314 from updatefiles:pubmed22n1165.xml\n",
      "Parsing finished. 26114 articles parsed.Total time: 9.790120363235474\n",
      "Parsing 37/314 from updatefiles:pubmed22n1206.xml\n",
      "Parsing finished. 25209 articles parsed.Total time: 9.946953535079956\n",
      "Parsing 38/314 from updatefiles:pubmed22n1399.xml\n",
      "Parsing finished. 5262 articles parsed.Total time: 1.828495979309082\n",
      "Parsing 39/314 from updatefiles:pubmed22n1192.xml\n",
      "Parsing finished. 28417 articles parsed.Total time: 9.195149898529053\n",
      "Parsing 40/314 from updatefiles:pubmed22n1312.xml\n",
      "Parsing finished. 28181 articles parsed.Total time: 10.398619651794434\n",
      "Parsing 41/314 from updatefiles:pubmed22n1406.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.251837253570557\n",
      "Parsing 42/314 from updatefiles:pubmed22n1329.xml\n",
      "Parsing finished. 22533 articles parsed.Total time: 6.613964796066284\n",
      "Parsing 43/314 from updatefiles:pubmed22n1115.xml\n",
      "Parsing finished. 15885 articles parsed.Total time: 4.338744163513184\n",
      "Parsing 44/314 from updatefiles:pubmed22n1132.xml\n",
      "Parsing finished. 28159 articles parsed.Total time: 10.237467765808105\n",
      "Parsing 45/314 from updatefiles:pubmed22n1222.xml\n",
      "Parsing finished. 15117 articles parsed.Total time: 4.334007740020752\n",
      "Parsing 46/314 from updatefiles:pubmed22n1335.xml\n",
      "Parsing finished. 25129 articles parsed.Total time: 8.42466950416565\n",
      "Parsing 47/314 from updatefiles:pubmed22n1424.xml\n",
      "Parsing finished. 26198 articles parsed.Total time: 11.109065055847168\n",
      "Parsing 48/314 from updatefiles:pubmed22n1244.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.627117156982422\n",
      "Parsing 49/314 from updatefiles:pubmed22n1224.xml\n",
      "Parsing finished. 24567 articles parsed.Total time: 10.075706720352173\n",
      "Parsing 50/314 from updatefiles:pubmed22n1183.xml\n",
      "Parsing finished. 27796 articles parsed.Total time: 10.931613445281982\n",
      "Parsing 51/314 from updatefiles:pubmed22n1239.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.981837511062622\n",
      "Parsing 52/314 from updatefiles:pubmed22n1308.xml\n",
      "Parsing finished. 18306 articles parsed.Total time: 6.085686922073364\n",
      "Parsing 53/314 from updatefiles:pubmed22n1321.xml\n",
      "Parsing finished. 27430 articles parsed.Total time: 10.248026847839355\n",
      "Parsing 54/314 from updatefiles:pubmed22n1314.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.354958057403564\n",
      "Parsing 55/314 from updatefiles:pubmed22n1181.xml\n",
      "Parsing finished. 19784 articles parsed.Total time: 6.620669364929199\n",
      "Parsing 56/314 from updatefiles:pubmed22n1351.xml\n",
      "Parsing finished. 20532 articles parsed.Total time: 6.378360033035278\n",
      "Parsing 57/314 from updatefiles:pubmed22n1193.xml\n",
      "Parsing finished. 20530 articles parsed.Total time: 7.455542802810669\n",
      "Parsing 58/314 from updatefiles:pubmed22n1247.xml\n",
      "Parsing finished. 1190 articles parsed.Total time: 0.34717297554016113\n",
      "Parsing 59/314 from updatefiles:pubmed22n1236.xml\n",
      "Parsing finished. 24930 articles parsed.Total time: 8.267950534820557\n",
      "Parsing 60/314 from updatefiles:pubmed22n1405.xml\n",
      "Parsing finished. 2573 articles parsed.Total time: 0.7090516090393066\n",
      "Parsing 61/314 from updatefiles:pubmed22n1330.xml\n",
      "Parsing finished. 21953 articles parsed.Total time: 8.050716876983643\n",
      "Parsing 62/314 from updatefiles:pubmed22n1415.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.949290990829468\n",
      "Parsing 63/314 from updatefiles:pubmed22n1396.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 15.486310720443726\n",
      "Parsing 64/314 from updatefiles:pubmed22n1389.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 16.286437273025513\n",
      "Parsing 65/314 from updatefiles:pubmed22n1173.xml\n",
      "Parsing finished. 4981 articles parsed.Total time: 1.4689710140228271\n",
      "Parsing 66/314 from updatefiles:pubmed22n1381.xml\n",
      "Parsing finished. 7553 articles parsed.Total time: 2.499537944793701\n",
      "Parsing 67/314 from updatefiles:pubmed22n1373.xml\n",
      "Parsing finished. 11852 articles parsed.Total time: 3.7112972736358643\n",
      "Parsing 68/314 from updatefiles:pubmed22n1380.xml\n",
      "Parsing finished. 21103 articles parsed.Total time: 7.437373399734497\n",
      "Parsing 69/314 from updatefiles:pubmed22n1128.xml\n",
      "Parsing finished. 6131 articles parsed.Total time: 1.907740592956543\n",
      "Parsing 70/314 from updatefiles:pubmed22n1148.xml\n",
      "Parsing finished. 29186 articles parsed.Total time: 12.899606943130493\n",
      "Parsing 71/314 from updatefiles:pubmed22n1280.xml\n",
      "Parsing finished. 28755 articles parsed.Total time: 10.232882261276245\n",
      "Parsing 72/314 from updatefiles:pubmed22n1295.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.564590454101562\n",
      "Parsing 73/314 from updatefiles:pubmed22n1194.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.569813013076782\n",
      "Parsing 74/314 from updatefiles:pubmed22n1158.xml\n",
      "Parsing finished. 18906 articles parsed.Total time: 6.9244091510772705\n",
      "Parsing 75/314 from updatefiles:pubmed22n1370.xml\n",
      "Parsing finished. 19048 articles parsed.Total time: 7.816479206085205\n",
      "Parsing 76/314 from updatefiles:pubmed22n1172.xml\n",
      "Parsing finished. 17099 articles parsed.Total time: 6.922020435333252\n",
      "Parsing 77/314 from updatefiles:pubmed22n1152.xml\n",
      "Parsing finished. 27633 articles parsed.Total time: 10.66865849494934\n",
      "Parsing 78/314 from updatefiles:pubmed22n1151.xml\n",
      "Parsing finished. 21207 articles parsed.Total time: 6.754696607589722\n",
      "Parsing 79/314 from updatefiles:pubmed22n1200.xml\n",
      "Parsing finished. 21932 articles parsed.Total time: 8.558509349822998\n",
      "Parsing 80/314 from updatefiles:pubmed22n1401.xml\n",
      "Parsing finished. 23354 articles parsed.Total time: 8.323637247085571\n",
      "Parsing 81/314 from updatefiles:pubmed22n1326.xml\n",
      "Parsing finished. 5456 articles parsed.Total time: 1.596242904663086\n",
      "Parsing 82/314 from updatefiles:pubmed22n1216.xml\n",
      "Parsing finished. 16074 articles parsed.Total time: 5.686028957366943\n",
      "Parsing 83/314 from updatefiles:pubmed22n1333.xml\n",
      "Parsing finished. 3221 articles parsed.Total time: 1.0573172569274902\n",
      "Parsing 84/314 from updatefiles:pubmed22n1159.xml\n",
      "Parsing finished. 17164 articles parsed.Total time: 6.6774537563323975\n",
      "Parsing 85/314 from updatefiles:pubmed22n1391.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.246786117553711\n",
      "Parsing 86/314 from updatefiles:pubmed22n1269.xml\n",
      "Parsing finished. 1431 articles parsed.Total time: 0.44434285163879395\n",
      "Parsing 87/314 from updatefiles:pubmed22n1318.xml\n",
      "Parsing finished. 18214 articles parsed.Total time: 6.251507759094238\n",
      "Parsing 88/314 from updatefiles:pubmed22n1358.xml\n",
      "Parsing finished. 4307 articles parsed.Total time: 1.5664892196655273\n",
      "Parsing 89/314 from updatefiles:pubmed22n1257.xml\n",
      "Parsing finished. 28109 articles parsed.Total time: 10.261234521865845\n",
      "Parsing 90/314 from updatefiles:pubmed22n1253.xml\n",
      "Parsing finished. 25311 articles parsed.Total time: 8.045410394668579\n",
      "Parsing 91/314 from updatefiles:pubmed22n1230.xml\n",
      "Parsing finished. 3686 articles parsed.Total time: 1.1191074848175049\n",
      "Parsing 92/314 from updatefiles:pubmed22n1286.xml\n",
      "Parsing finished. 4563 articles parsed.Total time: 2.284189224243164\n",
      "Parsing 93/314 from updatefiles:pubmed22n1220.xml\n",
      "Parsing finished. 9888 articles parsed.Total time: 3.617394208908081\n",
      "Parsing 94/314 from updatefiles:pubmed22n1130.xml\n",
      "Parsing finished. 11439 articles parsed.Total time: 4.352480173110962\n",
      "Parsing 95/314 from updatefiles:pubmed22n1403.xml\n",
      "Parsing finished. 22668 articles parsed.Total time: 7.083043575286865\n",
      "Parsing 96/314 from updatefiles:pubmed22n1361.xml\n",
      "Parsing finished. 7731 articles parsed.Total time: 2.6987102031707764\n",
      "Parsing 97/314 from updatefiles:pubmed22n1359.xml\n",
      "Parsing finished. 21487 articles parsed.Total time: 8.01732587814331\n",
      "Parsing 98/314 from updatefiles:pubmed22n1157.xml\n",
      "Parsing finished. 25831 articles parsed.Total time: 9.757441759109497\n",
      "Parsing 99/314 from updatefiles:pubmed22n1156.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 16.134111166000366\n",
      "Parsing 100/314 from updatefiles:pubmed22n1171.xml\n",
      "Parsing finished. 19813 articles parsed.Total time: 6.868310451507568\n",
      "Parsing 101/314 from updatefiles:pubmed22n1379.xml\n",
      "Parsing finished. 7505 articles parsed.Total time: 3.1081907749176025\n",
      "Parsing 102/314 from updatefiles:pubmed22n1184.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.242548704147339\n",
      "Parsing 103/314 from updatefiles:pubmed22n1263.xml\n",
      "Parsing finished. 24180 articles parsed.Total time: 9.153459072113037\n",
      "Parsing 104/314 from updatefiles:pubmed22n1402.xml\n",
      "Parsing finished. 21215 articles parsed.Total time: 7.803406476974487\n",
      "Parsing 105/314 from updatefiles:pubmed22n1252.xml\n",
      "Parsing finished. 21308 articles parsed.Total time: 7.459196329116821\n",
      "Parsing 106/314 from updatefiles:pubmed22n1378.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 14.135340690612793\n",
      "Parsing 107/314 from updatefiles:pubmed22n1116.xml\n",
      "Parsing finished. 27261 articles parsed.Total time: 9.811175346374512\n",
      "Parsing 108/314 from updatefiles:pubmed22n1261.xml\n",
      "Parsing finished. 5575 articles parsed.Total time: 1.66227388381958\n",
      "Parsing 109/314 from updatefiles:pubmed22n1225.xml\n",
      "Parsing finished. 22332 articles parsed.Total time: 7.3771092891693115\n",
      "Parsing 110/314 from updatefiles:pubmed22n1354.xml\n",
      "Parsing finished. 17004 articles parsed.Total time: 5.956570148468018\n",
      "Parsing 111/314 from updatefiles:pubmed22n1282.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.842125415802002\n",
      "Parsing 112/314 from updatefiles:pubmed22n1392.xml\n",
      "Parsing finished. 23240 articles parsed.Total time: 8.221884965896606\n",
      "Parsing 113/314 from updatefiles:pubmed22n1383.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.919262409210205\n",
      "Parsing 114/314 from updatefiles:pubmed22n1281.xml\n",
      "Parsing finished. 23961 articles parsed.Total time: 8.914466619491577\n",
      "Parsing 115/314 from updatefiles:pubmed22n1149.xml\n",
      "Parsing finished. 7556 articles parsed.Total time: 2.8315961360931396\n",
      "Parsing 116/314 from updatefiles:pubmed22n1404.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.650702953338623\n",
      "Parsing 117/314 from updatefiles:pubmed22n1277.xml\n",
      "Parsing finished. 25180 articles parsed.Total time: 8.325151920318604\n",
      "Parsing 118/314 from updatefiles:pubmed22n1420.xml\n",
      "Parsing finished. 6189 articles parsed.Total time: 2.3553121089935303\n",
      "Parsing 119/314 from updatefiles:pubmed22n1248.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.037834405899048\n",
      "Parsing 120/314 from updatefiles:pubmed22n1296.xml\n",
      "Parsing finished. 3894 articles parsed.Total time: 1.1973168849945068\n",
      "Parsing 121/314 from updatefiles:pubmed22n1274.xml\n",
      "Parsing finished. 23084 articles parsed.Total time: 8.639153242111206\n",
      "Parsing 122/314 from updatefiles:pubmed22n1349.xml\n",
      "Parsing finished. 18389 articles parsed.Total time: 6.481853723526001\n",
      "Parsing 123/314 from updatefiles:pubmed22n1135.xml\n",
      "Parsing finished. 7027 articles parsed.Total time: 1.8705451488494873\n",
      "Parsing 124/314 from updatefiles:pubmed22n1408.xml\n",
      "Parsing finished. 7786 articles parsed.Total time: 3.4423141479492188\n",
      "Parsing 125/314 from updatefiles:pubmed22n1138.xml\n",
      "Parsing finished. 23536 articles parsed.Total time: 8.824783325195312\n",
      "Parsing 126/314 from updatefiles:pubmed22n1267.xml\n",
      "Parsing finished. 657 articles parsed.Total time: 0.21617364883422852\n",
      "Parsing 127/314 from updatefiles:pubmed22n1175.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 13.586672067642212\n",
      "Parsing 128/314 from updatefiles:pubmed22n1169.xml\n",
      "Parsing finished. 17717 articles parsed.Total time: 6.514252185821533\n",
      "Parsing 129/314 from updatefiles:pubmed22n1356.xml\n",
      "Parsing finished. 13077 articles parsed.Total time: 4.565911531448364\n",
      "Parsing 130/314 from updatefiles:pubmed22n1189.xml\n",
      "Parsing finished. 8035 articles parsed.Total time: 3.0439789295196533\n",
      "Parsing 131/314 from updatefiles:pubmed22n1311.xml\n",
      "Parsing finished. 5984 articles parsed.Total time: 2.0799753665924072\n",
      "Parsing 132/314 from updatefiles:pubmed22n1419.xml\n",
      "Parsing finished. 22677 articles parsed.Total time: 9.003430604934692\n",
      "Parsing 133/314 from updatefiles:pubmed22n1140.xml\n",
      "Parsing finished. 29433 articles parsed.Total time: 10.84522795677185\n",
      "Parsing 134/314 from updatefiles:pubmed22n1119.xml\n",
      "Parsing finished. 21680 articles parsed.Total time: 8.233055114746094\n",
      "Parsing 135/314 from updatefiles:pubmed22n1127.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.84570026397705\n",
      "Parsing 136/314 from updatefiles:pubmed22n1188.xml\n",
      "Parsing finished. 5803 articles parsed.Total time: 2.2538208961486816\n",
      "Parsing 137/314 from updatefiles:pubmed22n1411.xml\n",
      "Parsing finished. 18115 articles parsed.Total time: 6.67881178855896\n",
      "Parsing 138/314 from updatefiles:pubmed22n1369.xml\n",
      "Parsing finished. 22015 articles parsed.Total time: 8.930118322372437\n",
      "Parsing 139/314 from updatefiles:pubmed22n1400.xml\n",
      "Parsing finished. 18724 articles parsed.Total time: 7.755715370178223\n",
      "Parsing 140/314 from updatefiles:pubmed22n1155.xml\n",
      "Parsing finished. 1673 articles parsed.Total time: 0.5748326778411865\n",
      "Parsing 141/314 from updatefiles:pubmed22n1278.xml\n",
      "Parsing finished. 9493 articles parsed.Total time: 3.5151283740997314\n",
      "Parsing 142/314 from updatefiles:pubmed22n1324.xml\n",
      "Parsing finished. 2267 articles parsed.Total time: 0.6548759937286377\n",
      "Parsing 143/314 from updatefiles:pubmed22n1343.xml\n",
      "Parsing finished. 1605 articles parsed.Total time: 0.6400351524353027\n",
      "Parsing 144/314 from updatefiles:pubmed22n1266.xml\n",
      "Parsing finished. 1051 articles parsed.Total time: 0.4277074337005615\n",
      "Parsing 145/314 from updatefiles:pubmed22n1336.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 14.285358428955078\n",
      "Parsing 146/314 from updatefiles:pubmed22n1393.xml\n",
      "Parsing finished. 26830 articles parsed.Total time: 9.881939888000488\n",
      "Parsing 147/314 from updatefiles:pubmed22n1428.xml\n",
      "Parsing finished. 27038 articles parsed.Total time: 8.8446204662323\n",
      "Parsing 148/314 from updatefiles:pubmed22n1348.xml\n",
      "Parsing finished. 24266 articles parsed.Total time: 7.664903879165649\n",
      "Parsing 149/314 from updatefiles:pubmed22n1146.xml\n",
      "Parsing finished. 23662 articles parsed.Total time: 9.950192213058472\n",
      "Parsing 150/314 from updatefiles:pubmed22n1256.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.167480945587158\n",
      "Parsing 151/314 from updatefiles:pubmed22n1271.xml\n",
      "Parsing finished. 10152 articles parsed.Total time: 3.7570948600769043\n",
      "Parsing 152/314 from updatefiles:pubmed22n1137.xml\n",
      "Parsing finished. 25545 articles parsed.Total time: 9.67856216430664\n",
      "Parsing 153/314 from updatefiles:pubmed22n1290.xml\n",
      "Parsing finished. 522 articles parsed.Total time: 0.1265707015991211\n",
      "Parsing 154/314 from updatefiles:pubmed22n1297.xml\n",
      "Parsing finished. 4227 articles parsed.Total time: 1.2225673198699951\n",
      "Parsing 155/314 from updatefiles:pubmed22n1360.xml\n",
      "Parsing finished. 22356 articles parsed.Total time: 8.881117582321167\n",
      "Parsing 156/314 from updatefiles:pubmed22n1120.xml\n",
      "Parsing finished. 25464 articles parsed.Total time: 7.891371726989746\n",
      "Parsing 157/314 from updatefiles:pubmed22n1365.xml\n",
      "Parsing finished. 19483 articles parsed.Total time: 7.507184028625488\n",
      "Parsing 158/314 from updatefiles:pubmed22n1423.xml\n",
      "Parsing finished. 11660 articles parsed.Total time: 3.4612655639648438\n",
      "Parsing 159/314 from updatefiles:pubmed22n1270.xml\n",
      "Parsing finished. 18901 articles parsed.Total time: 6.7527546882629395\n",
      "Parsing 160/314 from updatefiles:pubmed22n1416.xml\n",
      "Parsing finished. 16057 articles parsed.Total time: 5.885766267776489\n",
      "Parsing 161/314 from updatefiles:pubmed22n1350.xml\n",
      "Parsing finished. 27666 articles parsed.Total time: 10.576797246932983\n",
      "Parsing 162/314 from updatefiles:pubmed22n1223.xml\n",
      "Parsing finished. 5289 articles parsed.Total time: 1.6663916110992432\n",
      "Parsing 163/314 from updatefiles:pubmed22n1168.xml\n",
      "Parsing finished. 16732 articles parsed.Total time: 6.7340850830078125\n",
      "Parsing 164/314 from updatefiles:pubmed22n1123.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.845882415771484\n",
      "Parsing 165/314 from updatefiles:pubmed22n1323.xml\n",
      "Parsing finished. 6709 articles parsed.Total time: 2.327423334121704\n",
      "Parsing 166/314 from updatefiles:pubmed22n1251.xml\n",
      "Parsing finished. 18403 articles parsed.Total time: 7.3873186111450195\n",
      "Parsing 167/314 from updatefiles:pubmed22n1160.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.614797830581665\n",
      "Parsing 168/314 from updatefiles:pubmed22n1288.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 16.96626377105713\n",
      "Parsing 169/314 from updatefiles:pubmed22n1388.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.476658344268799\n",
      "Parsing 170/314 from updatefiles:pubmed22n1250.xml\n",
      "Parsing finished. 10722 articles parsed.Total time: 4.105116128921509\n",
      "Parsing 171/314 from updatefiles:pubmed22n1418.xml\n",
      "Parsing finished. 23744 articles parsed.Total time: 9.023562669754028\n",
      "Parsing 172/314 from updatefiles:pubmed22n1166.xml\n",
      "Parsing finished. 7174 articles parsed.Total time: 2.5030617713928223\n",
      "Parsing 173/314 from updatefiles:pubmed22n1352.xml\n",
      "Parsing finished. 4397 articles parsed.Total time: 1.3907756805419922\n",
      "Parsing 174/314 from updatefiles:pubmed22n1202.xml\n",
      "Parsing finished. 13169 articles parsed.Total time: 5.083277463912964\n",
      "Parsing 175/314 from updatefiles:pubmed22n1327.xml\n",
      "Parsing finished. 4466 articles parsed.Total time: 1.4258332252502441\n",
      "Parsing 176/314 from updatefiles:pubmed22n1367.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.776551246643066\n",
      "Parsing 177/314 from updatefiles:pubmed22n1121.xml\n",
      "Parsing finished. 2776 articles parsed.Total time: 0.8920717239379883\n",
      "Parsing 178/314 from updatefiles:pubmed22n1316.xml\n",
      "Parsing finished. 2034 articles parsed.Total time: 0.6718697547912598\n",
      "Parsing 179/314 from updatefiles:pubmed22n1164.xml\n",
      "Parsing finished. 26593 articles parsed.Total time: 10.223558902740479\n",
      "Parsing 180/314 from updatefiles:pubmed22n1228.xml\n",
      "Parsing finished. 9005 articles parsed.Total time: 2.5529940128326416\n",
      "Parsing 181/314 from updatefiles:pubmed22n1227.xml\n",
      "Parsing finished. 19061 articles parsed.Total time: 6.6708714962005615\n",
      "Parsing 182/314 from updatefiles:pubmed22n1363.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.174537897109985\n",
      "Parsing 183/314 from updatefiles:pubmed22n1273.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 13.227121353149414\n",
      "Parsing 184/314 from updatefiles:pubmed22n1196.xml\n",
      "Parsing finished. 19000 articles parsed.Total time: 6.4477784633636475\n",
      "Parsing 185/314 from updatefiles:pubmed22n1268.xml\n",
      "Parsing finished. 29512 articles parsed.Total time: 11.40015983581543\n",
      "Parsing 186/314 from updatefiles:pubmed22n1287.xml\n",
      "Parsing finished. 18372 articles parsed.Total time: 5.754897832870483\n",
      "Parsing 187/314 from updatefiles:pubmed22n1154.xml\n",
      "Parsing finished. 3662 articles parsed.Total time: 1.1913485527038574\n",
      "Parsing 188/314 from updatefiles:pubmed22n1131.xml\n",
      "Parsing finished. 4101 articles parsed.Total time: 1.2450110912322998\n",
      "Parsing 189/314 from updatefiles:pubmed22n1124.xml\n",
      "Parsing finished. 3440 articles parsed.Total time: 1.2009186744689941\n",
      "Parsing 190/314 from updatefiles:pubmed22n1153.xml\n",
      "Parsing finished. 2544 articles parsed.Total time: 0.8007464408874512\n",
      "Parsing 191/314 from updatefiles:pubmed22n1232.xml\n",
      "Parsing finished. 6787 articles parsed.Total time: 2.2534008026123047\n",
      "Parsing 192/314 from updatefiles:pubmed22n1426.xml\n",
      "Parsing finished. 20900 articles parsed.Total time: 7.555207252502441\n",
      "Parsing 193/314 from updatefiles:pubmed22n1262.xml\n",
      "Parsing finished. 5797 articles parsed.Total time: 1.9273829460144043\n",
      "Parsing 194/314 from updatefiles:pubmed22n1328.xml\n",
      "Parsing finished. 14398 articles parsed.Total time: 5.189891815185547\n",
      "Parsing 195/314 from updatefiles:pubmed22n1371.xml\n",
      "Parsing finished. 28400 articles parsed.Total time: 13.37417221069336\n",
      "Parsing 196/314 from updatefiles:pubmed22n1412.xml\n",
      "Parsing finished. 4776 articles parsed.Total time: 1.2339115142822266\n",
      "Parsing 197/314 from updatefiles:pubmed22n1260.xml\n",
      "Parsing finished. 23777 articles parsed.Total time: 6.810962677001953\n",
      "Parsing 198/314 from updatefiles:pubmed22n1258.xml\n",
      "Parsing finished. 16902 articles parsed.Total time: 4.856236934661865\n",
      "Parsing 199/314 from updatefiles:pubmed22n1139.xml\n",
      "Parsing finished. 17523 articles parsed.Total time: 7.039515495300293\n",
      "Parsing 200/314 from updatefiles:pubmed22n1219.xml\n",
      "Parsing finished. 11624 articles parsed.Total time: 4.232185125350952\n",
      "Parsing 201/314 from updatefiles:pubmed22n1234.xml\n",
      "Parsing finished. 29271 articles parsed.Total time: 10.477996587753296\n",
      "Parsing 202/314 from updatefiles:pubmed22n1421.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 15.382163763046265\n",
      "Parsing 203/314 from updatefiles:pubmed22n1170.xml\n",
      "Parsing finished. 4502 articles parsed.Total time: 1.5292329788208008\n",
      "Parsing 204/314 from updatefiles:pubmed22n1161.xml\n",
      "Parsing finished. 1823 articles parsed.Total time: 0.4948384761810303\n",
      "Parsing 205/314 from updatefiles:pubmed22n1309.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.130418062210083\n",
      "Parsing 206/314 from updatefiles:pubmed22n1265.xml\n",
      "Parsing finished. 4294 articles parsed.Total time: 1.3508319854736328\n",
      "Parsing 207/314 from updatefiles:pubmed22n1284.xml\n",
      "Parsing finished. 29978 articles parsed.Total time: 12.155680418014526\n",
      "Parsing 208/314 from updatefiles:pubmed22n1215.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.072410345077515\n",
      "Parsing 209/314 from updatefiles:pubmed22n1317.xml\n",
      "Parsing finished. 6137 articles parsed.Total time: 1.919403076171875\n",
      "Parsing 210/314 from updatefiles:pubmed22n1214.xml\n",
      "Parsing finished. 3152 articles parsed.Total time: 0.869962215423584\n",
      "Parsing 211/314 from updatefiles:pubmed22n1212.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.620702505111694\n",
      "Parsing 212/314 from updatefiles:pubmed22n1342.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.096138954162598\n",
      "Parsing 213/314 from updatefiles:pubmed22n1211.xml\n",
      "Parsing finished. 3305 articles parsed.Total time: 1.1538043022155762\n",
      "Parsing 214/314 from updatefiles:pubmed22n1240.xml\n",
      "Parsing finished. 24212 articles parsed.Total time: 8.178166151046753\n",
      "Parsing 215/314 from updatefiles:pubmed22n1198.xml\n",
      "Parsing finished. 15160 articles parsed.Total time: 5.892842531204224\n",
      "Parsing 216/314 from updatefiles:pubmed22n1425.xml\n",
      "Parsing finished. 28432 articles parsed.Total time: 11.414813041687012\n",
      "Parsing 217/314 from updatefiles:pubmed22n1205.xml\n",
      "Parsing finished. 16110 articles parsed.Total time: 5.063194274902344\n",
      "Parsing 218/314 from updatefiles:pubmed22n1337.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.042685270309448\n",
      "Parsing 219/314 from updatefiles:pubmed22n1237.xml\n",
      "Parsing finished. 18463 articles parsed.Total time: 7.2225987911224365\n",
      "Parsing 220/314 from updatefiles:pubmed22n1141.xml\n",
      "Parsing finished. 24503 articles parsed.Total time: 9.667895078659058\n",
      "Parsing 221/314 from updatefiles:pubmed22n1186.xml\n",
      "Parsing finished. 25362 articles parsed.Total time: 7.272894382476807\n",
      "Parsing 222/314 from updatefiles:pubmed22n1384.xml\n",
      "Parsing finished. 26270 articles parsed.Total time: 9.7521333694458\n",
      "Parsing 223/314 from updatefiles:pubmed22n1322.xml\n",
      "Parsing finished. 20519 articles parsed.Total time: 7.319816827774048\n",
      "Parsing 224/314 from updatefiles:pubmed22n1306.xml\n",
      "Parsing finished. 29998 articles parsed.Total time: 12.620847225189209\n",
      "Parsing 225/314 from updatefiles:pubmed22n1298.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.80319619178772\n",
      "Parsing 226/314 from updatefiles:pubmed22n1233.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 13.711013317108154\n",
      "Parsing 227/314 from updatefiles:pubmed22n1339.xml\n",
      "Parsing finished. 2438 articles parsed.Total time: 0.6573770046234131\n",
      "Parsing 228/314 from updatefiles:pubmed22n1210.xml\n",
      "Parsing finished. 29017 articles parsed.Total time: 11.006361246109009\n",
      "Parsing 229/314 from updatefiles:pubmed22n1187.xml\n",
      "Parsing finished. 26176 articles parsed.Total time: 9.334871053695679\n",
      "Parsing 230/314 from updatefiles:pubmed22n1246.xml\n",
      "Parsing finished. 18956 articles parsed.Total time: 6.805241823196411\n",
      "Parsing 231/314 from updatefiles:pubmed22n1307.xml\n",
      "Parsing finished. 19831 articles parsed.Total time: 6.895081281661987\n",
      "Parsing 232/314 from updatefiles:pubmed22n1217.xml\n",
      "Parsing finished. 24418 articles parsed.Total time: 8.242738485336304\n",
      "Parsing 233/314 from updatefiles:pubmed22n1398.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.484210014343262\n",
      "Parsing 234/314 from updatefiles:pubmed22n1231.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.457254886627197\n",
      "Parsing 235/314 from updatefiles:pubmed22n1259.xml\n",
      "Parsing finished. 17108 articles parsed.Total time: 6.562485456466675\n",
      "Parsing 236/314 from updatefiles:pubmed22n1142.xml\n",
      "Parsing finished. 19660 articles parsed.Total time: 5.96515679359436\n",
      "Parsing 237/314 from updatefiles:pubmed22n1241.xml\n",
      "Parsing finished. 23245 articles parsed.Total time: 6.99120306968689\n",
      "Parsing 238/314 from updatefiles:pubmed22n1162.xml\n",
      "Parsing finished. 22442 articles parsed.Total time: 7.656069040298462\n",
      "Parsing 239/314 from updatefiles:pubmed22n1118.xml\n",
      "Parsing finished. 20980 articles parsed.Total time: 6.711939096450806\n",
      "Parsing 240/314 from updatefiles:pubmed22n1176.xml\n",
      "Parsing finished. 26504 articles parsed.Total time: 10.774959087371826\n",
      "Parsing 241/314 from updatefiles:pubmed22n1313.xml\n",
      "Parsing finished. 29998 articles parsed.Total time: 12.263000011444092\n",
      "Parsing 242/314 from updatefiles:pubmed22n1213.xml\n",
      "Parsing finished. 22053 articles parsed.Total time: 6.671751022338867\n",
      "Parsing 243/314 from updatefiles:pubmed22n1221.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.056786298751831\n",
      "Parsing 244/314 from updatefiles:pubmed22n1315.xml\n",
      "Parsing finished. 24355 articles parsed.Total time: 8.73433232307434\n",
      "Parsing 245/314 from updatefiles:pubmed22n1413.xml\n",
      "Parsing finished. 2583 articles parsed.Total time: 0.6874635219573975\n",
      "Parsing 246/314 from updatefiles:pubmed22n1303.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.715091705322266\n",
      "Parsing 247/314 from updatefiles:pubmed22n1167.xml\n",
      "Parsing finished. 22523 articles parsed.Total time: 9.4763662815094\n",
      "Parsing 248/314 from updatefiles:pubmed22n1310.xml\n",
      "Parsing finished. 25071 articles parsed.Total time: 10.422681093215942\n",
      "Parsing 249/314 from updatefiles:pubmed22n1410.xml\n",
      "Parsing finished. 22377 articles parsed.Total time: 8.939500331878662\n",
      "Parsing 250/314 from updatefiles:pubmed22n1245.xml\n",
      "Parsing finished. 18383 articles parsed.Total time: 6.110058307647705\n",
      "Parsing 251/314 from updatefiles:pubmed22n1372.xml\n",
      "Parsing finished. 27402 articles parsed.Total time: 8.928931951522827\n",
      "Parsing 252/314 from updatefiles:pubmed22n1129.xml\n",
      "Parsing finished. 18712 articles parsed.Total time: 6.400268316268921\n",
      "Parsing 253/314 from updatefiles:pubmed22n1332.xml\n",
      "Parsing finished. 3735 articles parsed.Total time: 1.123746633529663\n",
      "Parsing 254/314 from updatefiles:pubmed22n1178.xml\n",
      "Parsing finished. 11040 articles parsed.Total time: 3.8830342292785645\n",
      "Parsing 255/314 from updatefiles:pubmed22n1272.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 13.290154933929443\n",
      "Parsing 256/314 from updatefiles:pubmed22n1235.xml\n",
      "Parsing finished. 19651 articles parsed.Total time: 6.090933799743652\n",
      "Parsing 257/314 from updatefiles:pubmed22n1203.xml\n",
      "Parsing finished. 7032 articles parsed.Total time: 2.2789883613586426\n",
      "Parsing 258/314 from updatefiles:pubmed22n1294.xml\n",
      "Parsing finished. 18364 articles parsed.Total time: 5.469099760055542\n",
      "Parsing 259/314 from updatefiles:pubmed22n1125.xml\n",
      "Parsing finished. 703 articles parsed.Total time: 0.1974945068359375\n",
      "Parsing 260/314 from updatefiles:pubmed22n1122.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.265779733657837\n",
      "Parsing 261/314 from updatefiles:pubmed22n1285.xml\n",
      "Parsing finished. 7369 articles parsed.Total time: 2.5826101303100586\n",
      "Parsing 262/314 from updatefiles:pubmed22n1366.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.399074792861938\n",
      "Parsing 263/314 from updatefiles:pubmed22n1207.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 13.153740644454956\n",
      "Parsing 264/314 from updatefiles:pubmed22n1395.xml\n",
      "Parsing finished. 20853 articles parsed.Total time: 7.765140533447266\n",
      "Parsing 265/314 from updatefiles:pubmed22n1355.xml\n",
      "Parsing finished. 24196 articles parsed.Total time: 9.383647918701172\n",
      "Parsing 266/314 from updatefiles:pubmed22n1300.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.603352546691895\n",
      "Parsing 267/314 from updatefiles:pubmed22n1283.xml\n",
      "Parsing finished. 23217 articles parsed.Total time: 8.157652854919434\n",
      "Parsing 268/314 from updatefiles:pubmed22n1346.xml\n",
      "Parsing finished. 22383 articles parsed.Total time: 7.5042173862457275\n",
      "Parsing 269/314 from updatefiles:pubmed22n1377.xml\n",
      "Parsing finished. 24021 articles parsed.Total time: 8.889562606811523\n",
      "Parsing 270/314 from updatefiles:pubmed22n1417.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 10.554226398468018\n",
      "Parsing 271/314 from updatefiles:pubmed22n1291.xml\n",
      "Parsing finished. 14464 articles parsed.Total time: 4.376109600067139\n",
      "Parsing 272/314 from updatefiles:pubmed22n1376.xml\n",
      "Parsing finished. 12100 articles parsed.Total time: 3.8656859397888184\n",
      "Parsing 273/314 from updatefiles:pubmed22n1341.xml\n",
      "Parsing finished. 18871 articles parsed.Total time: 6.574864625930786\n",
      "Parsing 274/314 from updatefiles:pubmed22n1386.xml\n",
      "Parsing finished. 27851 articles parsed.Total time: 10.411275386810303\n",
      "Parsing 275/314 from updatefiles:pubmed22n1190.xml\n",
      "Parsing finished. 23644 articles parsed.Total time: 8.572737455368042\n",
      "Parsing 276/314 from updatefiles:pubmed22n1427.xml\n",
      "Parsing finished. 28522 articles parsed.Total time: 10.951208114624023\n",
      "Parsing 277/314 from updatefiles:pubmed22n1218.xml\n",
      "Parsing finished. 28362 articles parsed.Total time: 11.10704255104065\n",
      "Parsing 278/314 from updatefiles:pubmed22n1414.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.148288249969482\n",
      "Parsing 279/314 from updatefiles:pubmed22n1242.xml\n",
      "Parsing finished. 10038 articles parsed.Total time: 3.487436532974243\n",
      "Parsing 280/314 from updatefiles:pubmed22n1276.xml\n",
      "Parsing finished. 18387 articles parsed.Total time: 7.405719041824341\n",
      "Parsing 281/314 from updatefiles:pubmed22n1191.xml\n",
      "Parsing finished. 22823 articles parsed.Total time: 7.787120819091797\n",
      "Parsing 282/314 from updatefiles:pubmed22n1347.xml\n",
      "Parsing finished. 2547 articles parsed.Total time: 0.7783935070037842\n",
      "Parsing 283/314 from updatefiles:pubmed22n1208.xml\n",
      "Parsing finished. 4416 articles parsed.Total time: 1.3373668193817139\n",
      "Parsing 284/314 from updatefiles:pubmed22n1374.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 13.918914794921875\n",
      "Parsing 285/314 from updatefiles:pubmed22n1340.xml\n",
      "Parsing finished. 27704 articles parsed.Total time: 10.61941123008728\n",
      "Parsing 286/314 from updatefiles:pubmed22n1143.xml\n",
      "Parsing finished. 28910 articles parsed.Total time: 10.371674299240112\n",
      "Parsing 287/314 from updatefiles:pubmed22n1331.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 15.563282489776611\n",
      "Parsing 288/314 from updatefiles:pubmed22n1387.xml\n",
      "Parsing finished. 12551 articles parsed.Total time: 4.281816244125366\n",
      "Parsing 289/314 from updatefiles:pubmed22n1305.xml\n",
      "Parsing finished. 23078 articles parsed.Total time: 7.5231993198394775\n",
      "Parsing 290/314 from updatefiles:pubmed22n1368.xml\n",
      "Parsing finished. 25259 articles parsed.Total time: 14.646912336349487\n",
      "Parsing 291/314 from updatefiles:pubmed22n1201.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 9.755113363265991\n",
      "Parsing 292/314 from updatefiles:pubmed22n1302.xml\n",
      "Parsing finished. 20232 articles parsed.Total time: 7.582873106002808\n",
      "Parsing 293/314 from updatefiles:pubmed22n1180.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.655693769454956\n",
      "Parsing 294/314 from updatefiles:pubmed22n1177.xml\n",
      "Parsing finished. 4485 articles parsed.Total time: 1.301002025604248\n",
      "Parsing 295/314 from updatefiles:pubmed22n1238.xml\n",
      "Parsing finished. 28833 articles parsed.Total time: 10.775774717330933\n",
      "Parsing 296/314 from updatefiles:pubmed22n1133.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.907924175262451\n",
      "Parsing 297/314 from updatefiles:pubmed22n1275.xml\n",
      "Parsing finished. 17115 articles parsed.Total time: 6.978571891784668\n",
      "Parsing 298/314 from updatefiles:pubmed22n1144.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.445531606674194\n",
      "Parsing 299/314 from updatefiles:pubmed22n1407.xml\n",
      "Parsing finished. 21875 articles parsed.Total time: 8.21598505973816\n",
      "Parsing 300/314 from updatefiles:pubmed22n1209.xml\n",
      "Parsing finished. 19812 articles parsed.Total time: 7.425982713699341\n",
      "Parsing 301/314 from updatefiles:pubmed22n1136.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 12.26587963104248\n",
      "Parsing 302/314 from updatefiles:pubmed22n1304.xml\n",
      "Parsing finished. 5217 articles parsed.Total time: 1.5460615158081055\n",
      "Parsing 303/314 from updatefiles:pubmed22n1289.xml\n",
      "Parsing finished. 8068 articles parsed.Total time: 2.403575897216797\n",
      "Parsing 304/314 from updatefiles:pubmed22n1229.xml\n",
      "Parsing finished. 29168 articles parsed.Total time: 11.342027187347412\n",
      "Parsing 305/314 from updatefiles:pubmed22n1325.xml\n",
      "Parsing finished. 24252 articles parsed.Total time: 7.316477537155151\n",
      "Parsing 306/314 from updatefiles:pubmed22n1385.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.85107421875\n",
      "Parsing 307/314 from updatefiles:pubmed22n1226.xml\n",
      "Parsing finished. 17324 articles parsed.Total time: 6.192119121551514\n",
      "Parsing 308/314 from updatefiles:pubmed22n1357.xml\n",
      "Parsing finished. 27752 articles parsed.Total time: 9.348528623580933\n",
      "Parsing 309/314 from updatefiles:pubmed22n1249.xml\n",
      "Parsing finished. 29999 articles parsed.Total time: 11.727277755737305\n",
      "Parsing 310/314 from updatefiles:pubmed22n1147.xml\n",
      "Parsing finished. 26859 articles parsed.Total time: 8.305988311767578\n",
      "Parsing 311/314 from updatefiles:pubmed22n1375.xml\n",
      "Parsing finished. 24968 articles parsed.Total time: 9.954488277435303\n",
      "Parsing 312/314 from updatefiles:pubmed22n1179.xml\n",
      "Parsing finished. 10767 articles parsed.Total time: 3.5648059844970703\n",
      "Parsing 313/314 from updatefiles:pubmed22n1243.xml\n",
      "Parsing finished. 20710 articles parsed.Total time: 7.423116683959961\n",
      "Parsing 314/314 from updatefiles:pubmed22n1204.xml\n",
      "<><> Parsing finished, results dumped to ./data/pubmed.json <><>\n",
      "<><> TOTAL TIME: 14994.696175s <><>\n"
     ]
    }
   ],
   "source": [
    "!python '02_run_parsing.py'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 3. Map MeSH to PMID (for document-category relationships)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "MeSH to PMID mapping is running...\n",
      "Exporting MeSH to PMID mappingp to MeSH terms\n",
      "Finished MeSH to PMID mapping. Time = 17.583333333333332 minutes\n",
      "MeSH to PMID mapping stat is running.\n"
     ]
    }
   ],
   "source": [
    "!python '03_run_mesh2pmid.py'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 243,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "MeSH to PMID mapping is running...\n",
      "Exporting MeSH to PMID mapping\n",
      "Finished MeSH to PMID mapping. Time = 17.166666666666668 minutes\n",
      "MeSH to PMID mapping stat is running.\n"
     ]
    }
   ],
   "source": [
    "!python '03_run_mesh2pmid.py'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 4 & 5. Index the documents (for document-entity relationships)\n",
    "Make sure Elasticsearch is properly configured and running first.\n",
    "4. Initialize the index. \n",
    "5. Run the index.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 114,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Deleted index: pubmed_x \r\n",
      "Response: {'acknowledged': True} \r\n",
      "\r\n"
     ]
    }
   ],
   "source": [
    "!python '04_run_index_init.py'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "50000 documents indexed in 0.181 minutes\n",
      "100000 documents indexed in 0.292 minutes\n",
      "150000 documents indexed in 0.472 minutes\n",
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     ]
    }
   ],
   "source": [
    "!python '05_run_index_populate.py'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Project-Specific Steps\n",
    "These steps should be customized for the project"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 6. Categorize the documents of interest"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 58,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "8 categories:  ['IHD', 'CM', 'ARR', 'VD', 'CHD', 'CCD', 'VOO', 'OTH']\n",
      "Collecting categories' subcategory MeSH terms...\n",
      "Textcube category to PMID mapping is being created....\n",
      "Textcube PMID to category mapping is being created....nds\n",
      "Textcube category statistics is being created....\n",
      "\n",
      "Category: Documents\n",
      "===================\n",
      "IHD: 235,278\n",
      "CM: 230,362\n",
      "ARR: 150,600\n",
      "VD: 132,444\n",
      "CHD: 461,353\n",
      "CCD: 98,623\n",
      "VOO: 40,896\n",
      "OTH: 209,154\n",
      "TOTAL: 1,157,787\n"
     ]
    }
   ],
   "source": [
    "!python '06_run_textcube.py'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 7. Vary the synonyms' cases\n",
    "Makes case-senstivie variations of the synonyms. This increases discovery of the synonyms within the case-sensitive text."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 90,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Running jobs...\n",
      "Done! 1 progress: 15 / 15\n"
     ]
    }
   ],
   "source": [
    "! python '07_run_vary_synonyms_cases.py'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 8. Count all synonyms in the indexed text\n",
    "This counts the case-varied synonyms."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 103,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Synonym count is running .....\n",
      "Running jobs. 0.0 seconds\n",
      "10030  synonyms successfully counted! 56.7 seconds\n"
     ]
    }
   ],
   "source": [
    "! python '08_run_count_synonyms.py'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 9. Screen for ambiguous synonyms\n",
    "Some synonyms will likely be ambiguous, leading to false positives. This step identifies the synonyms presumed be potentially ambiguous (i.e. short synonyms, synonyms that are single English words)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 104,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Running jobs...\n",
      "Exporting the suspect synonyms to data/remove_these_synonyms.txt\n",
      "Inspect this file when the process is complete\n",
      "\n",
      "Synonyms in data/remove_these_synonyms.txt will be removed. Check here.\n"
     ]
    }
   ],
   "source": [
    "! python '09_run_screen_synonyms.py'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Next steps:\n",
    "- Add/remove synonyms as described in the next block\n",
    "- Run steps 10-13. \n",
    "- Inspect the scores. \n",
    "- Add/remove synonyms again\n",
    "- Repeat the process until you're satisfied."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Modify the file from step 9 (data/remove_these_synonyms.txt). \n",
    "Add bad synonyms, remove good synonyms. The case-varied versions are in here. The first part has synonyms that are English words. The second part has synonyms that are very short.\n",
    "- If you add, add the case-varied versions (e.g., \"Added Protein\", \"added protein\", \"Added protein\", \"added Protein\"). \n",
    "- If you remove, remove the case-varied versions of the entity."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "###  10. Get the entity counts\n",
    "Using the synonyms that aren't bad synonyms and their synonym counts, this assemble the entity counts"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 110,
   "metadata": {},
   "outputs": [],
   "source": [
    "! python '10_run_make_entity_counts.py'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 11. Update the metadata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 111,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Updating the PMID -to-> Entity Count dictionary\n",
      "Updating the Category -to-> Entity-Containing-PMID dictionary\n"
     ]
    }
   ],
   "source": [
    "!python '11_run_metadata_update.py'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "### 12. Produce CaseOLAP scores for the entities"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 112,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Category: # PMIDs collected\n",
      "===========================\n",
      "IHD: 3677 PMIDs\n",
      "CM: 1632 PMIDs\n",
      "ARR: 339 PMIDs\n",
      "VD: 447 PMIDs\n",
      "CHD: 4636 PMIDs\n",
      "CCD: 590 PMIDs\n",
      "VOO: 92 PMIDs\n",
      "OTH: 1957 PMIDs\n",
      "\n",
      "Category: # Entities Found\n",
      "==========================\n",
      "IHD 53\n",
      "CM 48\n",
      "ARR 28\n",
      "VD 33\n",
      "CHD 48\n",
      "CCD 39\n",
      "VOO 16\n",
      "OTH 55\n",
      "Total entities: 65\n"
     ]
    }
   ],
   "source": [
    "!python '12_run_caseolap_score.py'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 13. Inspect entity scores\n",
    "- You may notice that some entities score highly due to false positive synonyms. In that case, go back to the file mentioned just before step 9. Add the bad synonyms to the list, and run steps 10-13 again until you are satisfied with the quality of the results.\n",
    "- Check the files in in *results/ranked_entities* and *results/ranked_synonyms* (unless you changed where they're stored)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 108,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "65/117 (Found/Searched) Entities \n",
      "55.56%\n",
      "\n",
      "Format:\n",
      "# [Rank] [ID] | Score [x.xxxx]\n",
      "===============================\n",
      "#counts in all categories: synonym\n",
      "\n",
      "\n",
      "*********************************\n",
      "******** Ranked Entities ********\n",
      "*********************************\n",
      "\n",
      "#1 P17302 | 0.7613 Total CaseOLAP Score\n",
      "=============================================\n",
      "3179: Cx43\n",
      "809: connexin-43\n",
      "165: Connexin-43\n",
      "\n",
      "#2 Q92736 | 0.7398 Total CaseOLAP Score\n",
      "=============================================\n",
      "2680: RyR2\n",
      "150: ryanodine receptor 2\n",
      "27: type 2 ryanodine receptor\n",
      "11: Ryanodine receptor 2\n",
      "8: Ryanodine Receptor 2\n",
      "6: Type 2 ryanodine receptor\n",
      "2: RYR-2\n",
      "1: cardiac muscle ryanodine receptor\n",
      "\n",
      "#3 P29474 | 0.7384 Total CaseOLAP Score\n",
      "=============================================\n",
      "4994: eNOS\n",
      "152: endothelial NOS\n",
      "90: cNOS\n",
      "21: constitutive NOS\n",
      "10: Endothelial NOS\n",
      "8: NOSIII\n",
      "2: 1.14.13.39\n",
      "1: Constitutive NOS\n",
      "1: nitric oxide synthase, endothelial\n",
      "\n",
      "#4 P19429 | 0.7103 Total CaseOLAP Score\n",
      "=============================================\n",
      "3363: cardiac troponin I\n",
      "476: Cardiac troponin I\n",
      "130: Cardiac Troponin I\n",
      "76: cardiac Troponin I\n",
      "1: troponin I, cardiac muscle\n",
      "\n",
      "#5 P14780 | 0.7102 Total CaseOLAP Score\n",
      "=============================================\n",
      "3444: MMP-9\n",
      "608: matrix metalloproteinase-9\n",
      "75: Matrix metalloproteinase-9\n",
      "31: gelatinase B\n",
      "17: Matrix Metalloproteinase-9\n",
      "8: 92 kDa gelatinase\n",
      "4: Gelatinase B\n",
      "1: 92 kDa type IV collagenase\n",
      "\n",
      "#6 P11532 | 0.6166 Total CaseOLAP Score\n",
      "=============================================\n",
      "1589: dystrophin\n",
      "150: Dystrophin\n",
      "\n",
      "#7 A0A075B6G3 | 0.6166 Total CaseOLAP Score\n",
      "=============================================\n",
      "1589: dystrophin\n",
      "150: Dystrophin\n",
      "\n",
      "#8 P01160 | 0.5819 Total CaseOLAP Score\n",
      "=============================================\n",
      "1164: proANP\n",
      "80: proANF\n",
      "13: cardiodilatin\n",
      "11: atrial natriuretic factor prohormone\n",
      "7: natriuretic peptides A\n",
      "4: atrial natriuretic peptide prohormone\n",
      "4: preproANP\n",
      "1: Natriuretic Peptides A\n",
      "\n",
      "#9 P16615 | 0.5105 Total CaseOLAP Score\n",
      "=============================================\n",
      "744: SERCA2\n",
      "3: sarcoplasmic/endoplasmic reticulum calcium ATPase 2\n",
      "\n",
      "#10 P26678 | 0.4976 Total CaseOLAP Score\n",
      "=============================================\n",
      "920: PLB\n",
      "7: cardiac phospholamban\n",
      "2: Cardiac phospholamban\n",
      "\n",
      "#11 Q5R352 | 0.4976 Total CaseOLAP Score\n",
      "=============================================\n",
      "920: PLB\n",
      "7: cardiac phospholamban\n",
      "2: Cardiac phospholamban\n",
      "\n",
      "#12 P05067 | 0.4428 Total CaseOLAP Score\n",
      "=============================================\n",
      "345: APP\n",
      "32: amyloid precursor protein\n",
      "14: ABPP\n",
      "12: CVAP\n",
      "2: amyloid-beta precursor protein\n",
      "1: Amyloid precursor protein\n",
      "1: APPI\n",
      "\n",
      "#13 P56539 | 0.4292 Total CaseOLAP Score\n",
      "=============================================\n",
      "268: caveolin-3\n",
      "70: Caveolin-3\n",
      "\n",
      "#14 P19634 | 0.4235 Total CaseOLAP Score\n",
      "=============================================\n",
      "489: NHE-1\n",
      "12: Na(+)/H(+) exchanger 1\n",
      "4: sodium/hydrogen exchanger 1\n",
      "\n",
      "#15 Q9NS61 | 0.3775 Total CaseOLAP Score\n",
      "=============================================\n",
      "228: KChIP2\n",
      "7: Kv channel-interacting protein 2\n",
      "2: Potassium Channel-Interacting Protein 2\n",
      "1: potassium channel-interacting protein 2\n",
      "\n",
      "#16 Q03135 | 0.3743 Total CaseOLAP Score\n",
      "=============================================\n",
      "210: caveolin-1\n",
      "41: Caveolin-1\n",
      "\n",
      "#17 Q01484 | 0.3590 Total CaseOLAP Score\n",
      "=============================================\n",
      "155: ankyrin-B\n",
      "35: Ankyrin-B\n",
      "3: ankyrin-2\n",
      "2: Ankyrin-2\n",
      "\n",
      "#18 P41180 | 0.3587 Total CaseOLAP Score\n",
      "=============================================\n",
      "221: CaSR\n",
      "64: CaR\n",
      "1: Extracellular calcium-sensing receptor\n",
      "1: extracellular calcium-sensing receptor\n",
      "\n",
      "#19 Q9BR39 | 0.3381 Total CaseOLAP Score\n",
      "=============================================\n",
      "78: junctophilin-2\n",
      "32: Junctophilin-2\n",
      "17: JP-2\n",
      "3: junctophilin type 2\n",
      "1: Junctophilin type 2\n",
      "\n",
      "#20 Q13061 | 0.3252 Total CaseOLAP Score\n",
      "=============================================\n",
      "134: triadin\n",
      "28: Triadin\n",
      "\n",
      "#21 P17252 | 0.3101 Total CaseOLAP Score\n",
      "=============================================\n",
      "153: PKC-alpha\n",
      "\n",
      "#22 P21817 | 0.2766 Total CaseOLAP Score\n",
      "=============================================\n",
      "76: RyR1\n",
      "8: skeletal muscle ryanodine receptor\n",
      "3: type 1 ryanodine receptor\n",
      "2: ryanodine receptor 1\n",
      "1: skeletal muscle calcium release channel\n",
      "\n",
      "#23 O14958 | 0.2758 Total CaseOLAP Score\n",
      "=============================================\n",
      "64: calsequestrin-2\n",
      "10: Calsequestrin-2\n",
      "\n",
      "#24 P11021 | 0.2332 Total CaseOLAP Score\n",
      "=============================================\n",
      "35: BiP\n",
      "21: GRP-78\n",
      "12: 78 kDa glucose-regulated protein\n",
      "4: binding-immunoglobulin protein\n",
      "1: immunoglobulin heavy chain-binding protein\n",
      "\n",
      "#25 Q14524 | 0.1912 Total CaseOLAP Score\n",
      "=============================================\n",
      "57: hH1\n",
      "\n",
      "#26 P56373 | 0.1848 Total CaseOLAP Score\n",
      "=============================================\n",
      "51: P2X3\n",
      "30: purinergic receptor\n",
      "4: ATP receptor\n",
      "2: Purinergic receptor\n",
      "1: Purinergic Receptor\n",
      "\n",
      "#27 Q12791 | 0.1815 Total CaseOLAP Score\n",
      "=============================================\n",
      "56: BK channel\n",
      "12: KCa1.1\n",
      "1: hSlo\n",
      "\n",
      "#28 P35212 | 0.1676 Total CaseOLAP Score\n",
      "=============================================\n",
      "55: Cx37\n",
      "20: connexin-37\n",
      "3: Connexin-37\n",
      "\n",
      "#29 P23634 | 0.1625 Total CaseOLAP Score\n",
      "=============================================\n",
      "24: PMCA4\n",
      "\n",
      "#30 P49768 | 0.1537 Total CaseOLAP Score\n",
      "=============================================\n",
      "16: presenilin-1\n",
      "10: PS-1\n",
      "5: Presenilin-1\n",
      "\n",
      "#31 P20073 | 0.1469 Total CaseOLAP Score\n",
      "=============================================\n",
      "15: annexin A7\n",
      "3: Annexin A7\n",
      "\n",
      "#32 P30626 | 0.1420 Total CaseOLAP Score\n",
      "=============================================\n",
      "38: sorcin\n",
      "21: Sorcin\n",
      "\n",
      "#33 P35609 | 0.1377 Total CaseOLAP Score\n",
      "=============================================\n",
      "13: alpha-actinin-2\n",
      "3: Alpha-Actinin-2\n",
      "1: Alpha-actinin-2\n",
      "\n",
      "#34 Q99828 | 0.1356 Total CaseOLAP Score\n",
      "=============================================\n",
      "16: CIB\n",
      "10: kinase-interacting protein\n",
      "3: calcium and integrin-binding protein 1\n",
      "2: Calcium- and integrin-binding protein\n",
      "2: Kinase-Interacting Protein\n",
      "2: KIP\n",
      "1: Calcium and integrin-binding protein 1\n",
      "1: calcium- and integrin-binding protein\n",
      "1: calmyrin\n",
      "\n",
      "#35 Q8TD43 | 0.1286 Total CaseOLAP Score\n",
      "=============================================\n",
      "12: melastatin-4\n",
      "3: Melastatin-4\n",
      "1: hTRPM4\n",
      "1: transient receptor potential cation channel subfamily M member 4\n",
      "\n",
      "#36 Q13563 | 0.1216 Total CaseOLAP Score\n",
      "=============================================\n",
      "15: polycystin-2\n",
      "2: Polycystin-2\n",
      "\n",
      "#37 O00499 | 0.1127 Total CaseOLAP Score\n",
      "=============================================\n",
      "9: bridging integrator 1\n",
      "4: Bridging integrator 1\n",
      "3: Amphiphysin II\n",
      "2: Bridging Integrator 1\n",
      "2: amphiphysin II\n",
      "\n",
      "#38 Q13586 | 0.1058 Total CaseOLAP Score\n",
      "=============================================\n",
      "12: stromal interaction molecule 1\n",
      "9: Stromal interaction molecule 1\n",
      "2: Stromal Interaction Molecule 1\n",
      "\n",
      "#39 Q13023 | 0.1007 Total CaseOLAP Score\n",
      "=============================================\n",
      "46: mAKAP\n",
      "\n",
      "#40 Q14571 | 0.0864 Total CaseOLAP Score\n",
      "=============================================\n",
      "14: InsP3R2\n",
      "2: type 2 inositol 1,4,5-trisphosphate receptor\n",
      "\n",
      "#41 Q16623 | 0.0685 Total CaseOLAP Score\n",
      "=============================================\n",
      "9: syntaxin-1A\n",
      "4: Syntaxin-1A\n",
      "\n",
      "#42 P0DP24 | 0.0649 Total CaseOLAP Score\n",
      "=============================================\n",
      "3: calmodulin-2\n",
      "1: Calmodulin-2\n",
      "\n",
      "#43 P68106 | 0.0616 Total CaseOLAP Score\n",
      "=============================================\n",
      "4: 12.6 kDa FK506-binding protein\n",
      "2: FKBP-12.6\n",
      "1: rotamase\n",
      "\n",
      "#44 E7EQ78 | 0.0596 Total CaseOLAP Score\n",
      "=============================================\n",
      "11: vanilloid receptor 1\n",
      "1: Vanilloid Receptor 1\n",
      "\n",
      "#45 P32418 | 0.0521 Total CaseOLAP Score\n",
      "=============================================\n",
      "5: sodium/calcium exchanger 1\n",
      "\n",
      "#46 P21796 | 0.0495 Total CaseOLAP Score\n",
      "=============================================\n",
      "4: VDAC-1\n",
      "1: voltage-dependent anion-selective channel protein 1\n",
      "\n",
      "#47 P49810 | 0.0456 Total CaseOLAP Score\n",
      "=============================================\n",
      "8: presenilin-2\n",
      "\n",
      "#48 P78417 | 0.0456 Total CaseOLAP Score\n",
      "=============================================\n",
      "2: 2.5.1.18\n",
      "1: glutathione S-transferase omega-1\n",
      "\n",
      "#49 P0DP23 | 0.0409 Total CaseOLAP Score\n",
      "=============================================\n",
      "2: Calmodulin-1\n",
      "1: calmodulin-1\n",
      "\n",
      "#50 Q9UBN4 | 0.0336 Total CaseOLAP Score\n",
      "=============================================\n",
      "12: TrpC4\n",
      "\n",
      "#51 Q13424 | 0.0303 Total CaseOLAP Score\n",
      "=============================================\n",
      "2: alpha-1-syntrophin\n",
      "\n",
      "#52 Q9ULB1 | 0.0278 Total CaseOLAP Score\n",
      "=============================================\n",
      "1: neurexin-1\n",
      "1: Neurexin-1\n",
      "\n",
      "#53 Q02790 | 0.0278 Total CaseOLAP Score\n",
      "=============================================\n",
      "1: rotamase\n",
      "1: FKBP59\n",
      "1: p59\n",
      "\n",
      "#54 P05556 | 0.0277 Total CaseOLAP Score\n",
      "=============================================\n",
      "3: glycoprotein IIa\n",
      "1: integrin beta-1\n",
      "\n",
      "#55 P06241 | 0.0272 Total CaseOLAP Score\n",
      "=============================================\n",
      "8: SLK\n",
      "\n",
      "#56 Q08209 | 0.0259 Total CaseOLAP Score\n",
      "=============================================\n",
      "2: calcineurin A alpha\n",
      "\n",
      "#57 O94759 | 0.0251 Total CaseOLAP Score\n",
      "=============================================\n",
      "1: transient receptor potential melastatin 2\n",
      "1: Transient receptor potential melastatin 2\n",
      "\n",
      "#58 P0DP25 | 0.0189 Total CaseOLAP Score\n",
      "=============================================\n",
      "1: calmodulin-3\n",
      "\n",
      "#59 Q9HDC5 | 0.0170 Total CaseOLAP Score\n",
      "=============================================\n",
      "2: junctophilin-1\n",
      "\n",
      "#60 P12814 | 0.0168 Total CaseOLAP Score\n",
      "=============================================\n",
      "1: Alpha-actinin-1\n",
      "\n",
      "#61 Q13557 | 0.0168 Total CaseOLAP Score\n",
      "=============================================\n",
      "1: calcium/calmodulin-dependent protein kinase type II subunit delta\n",
      "1: Calcium/calmodulin-dependent protein kinase type II subunit delta\n",
      "\n",
      "#62 P22460 | 0.0141 Total CaseOLAP Score\n",
      "=============================================\n",
      "1: Potassium voltage-gated channel subfamily A member 5\n",
      "1: Potassium Voltage-Gated Channel Subfamily A Member 5\n",
      "\n",
      "#63 O00141 | 0.0139 Total CaseOLAP Score\n",
      "=============================================\n",
      "1: serum/glucocorticoid-regulated kinase 1\n",
      "1: Serum/glucocorticoid-regulated kinase 1\n",
      "\n",
      "#64 O14649 | 0.0139 Total CaseOLAP Score\n",
      "=============================================\n",
      "1: potassium channel subfamily K member 3\n",
      "1: Potassium Channel Subfamily K Member 3\n",
      "\n",
      "#65 Q9NZV5 | 0.0130 Total CaseOLAP Score\n",
      "=============================================\n",
      "2: selenoprotein N\n"
     ]
    }
   ],
   "source": [
    "! python '13_run_inspect_entity_scores.py'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "NOTE: Watch out for making conclusions based on proteins that cluster tightly together. They might just be clustering together because they have the same synonyms (although they may have the same synonyms because they are similar, but that could have been determined \n",
    "without looking at the score)"
   ]
  }
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