stats.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "%load_ext autoreload\n",
    "%autoreload 2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os,sys\n",
    "sys.path.insert(0,\"../torchxrayvision/\")\n",
    "from glob import glob\n",
    "import matplotlib.pyplot as plt\n",
    "import numpy as np\n",
    "import torch\n",
    "import torchvision\n",
    "import sys\n",
    "import torch.nn.functional as F\n",
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "import torchxrayvision as xrv"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "dataset = xrv.datasets.COVID19_Dataset(imgpath=\"../covid-chestxray-dataset/images\",\n",
    "                                      csvpath=\"../covid-chestxray-dataset/metadata.csv\",\n",
    "                                      views=[\"PA\",\"AP\",\"AP Supine\"])\n",
    "                                      #views=[\"PA\",\"AP\",\"AP Supine\", \"L\"])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'Aspergillosis': {0.0: 677, 1.0: 2},\n",
      " 'Aspiration': {0.0: 678, 1.0: 1},\n",
      " 'Bacterial': {0.0: 628, 1.0: 51},\n",
      " 'COVID-19': {0.0: 211, 1.0: 468},\n",
      " 'Chlamydophila': {0.0: 678, 1.0: 1},\n",
      " 'E.Coli': {0.0: 675, 1.0: 4},\n",
      " 'Fungal': {0.0: 653, 1.0: 26},\n",
      " 'H1N1': {0.0: 678, 1.0: 1},\n",
      " 'Herpes ': {0.0: 676, 1.0: 3},\n",
      " 'Influenza': {0.0: 675, 1.0: 4},\n",
      " 'Klebsiella': {0.0: 670, 1.0: 9},\n",
      " 'Legionella': {0.0: 672, 1.0: 7},\n",
      " 'Lipoid': {0.0: 671, 1.0: 8},\n",
      " 'MERS-CoV': {0.0: 669, 1.0: 10},\n",
      " 'MRSA': {0.0: 678, 1.0: 1},\n",
      " 'Mycoplasma': {0.0: 674, 1.0: 5},\n",
      " 'No Finding': {0.0: 662, 1.0: 17},\n",
      " 'Nocardia': {0.0: 675, 1.0: 4},\n",
      " 'Pneumocystis': {0.0: 655, 1.0: 24},\n",
      " 'Pneumonia': {0.0: 28, 1.0: 651},\n",
      " 'SARS': {0.0: 663, 1.0: 16},\n",
      " 'Staphylococcus': {0.0: 678, 1.0: 1},\n",
      " 'Streptococcus': {0.0: 661, 1.0: 18},\n",
      " 'Tuberculosis': {0.0: 668, 1.0: 11},\n",
      " 'Varicella': {0.0: 674, 1.0: 5},\n",
      " 'Viral': {0.0: 173, 1.0: 506}}\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "COVID19_Dataset num_samples=679 views=['PA', 'AP', 'AP Supine']"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dataset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "dataset.csv = dataset.csv.reset_index()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "# csv = pd.read_csv(\"../covid-chestxray-dataset/metadata.csv\")\n",
    "# csv = csv[csv.view.isin([\"PA\",\"AP\",\"AP Supine\"])]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "412"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(set(dataset.csv[\"patientid\"]))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "labels = pd.DataFrame(dict(zip(dataset.pathologies, dataset.labels.T.astype(int))))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Index(['Aspergillosis', 'Aspiration', 'Bacterial', 'COVID-19', 'Chlamydophila',\n",
       "       'E.Coli', 'Fungal', 'H1N1', 'Herpes ', 'Influenza', 'Klebsiella',\n",
       "       'Legionella', 'Lipoid', 'MERS-CoV', 'MRSA', 'Mycoplasma', 'No Finding',\n",
       "       'Nocardia', 'Pneumocystis', 'Pneumonia', 'SARS', 'Staphylococcus',\n",
       "       'Streptococcus', 'Tuberculosis', 'Varicella', 'Viral'],\n",
       "      dtype='object')"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "labels.columns"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "M    230\n",
       "F    139\n",
       "Name: sex, dtype: int64"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dataset.csv.groupby(\"patientid\").first().sex.value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Finding</th>\n",
       "      <th>Type</th>\n",
       "      <th>Genus or Species</th>\n",
       "      <th>Subtype</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Pneumonia</td>\n",
       "      <td>Viral</td>\n",
       "      <td>COVID-19</td>\n",
       "      <td>Unknown</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Pneumonia</td>\n",
       "      <td>Viral</td>\n",
       "      <td>COVID-19</td>\n",
       "      <td>Unknown</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Pneumonia</td>\n",
       "      <td>Viral</td>\n",
       "      <td>COVID-19</td>\n",
       "      <td>Unknown</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Pneumonia</td>\n",
       "      <td>Viral</td>\n",
       "      <td>COVID-19</td>\n",
       "      <td>Unknown</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Pneumonia</td>\n",
       "      <td>Viral</td>\n",
       "      <td>COVID-19</td>\n",
       "      <td>Unknown</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>674</th>\n",
       "      <td>Pneumonia</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Unknown</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>675</th>\n",
       "      <td>Pneumonia</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Unknown</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>676</th>\n",
       "      <td>Pneumonia</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Unknown</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>677</th>\n",
       "      <td>Pneumonia</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Unknown</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>678</th>\n",
       "      <td>Pneumonia</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>Unknown</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>651 rows × 4 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       Finding     Type Genus or Species  Subtype\n",
       "0    Pneumonia    Viral         COVID-19  Unknown\n",
       "1    Pneumonia    Viral         COVID-19  Unknown\n",
       "2    Pneumonia    Viral         COVID-19  Unknown\n",
       "3    Pneumonia    Viral         COVID-19  Unknown\n",
       "4    Pneumonia    Viral         COVID-19  Unknown\n",
       "..         ...      ...              ...      ...\n",
       "674  Pneumonia  Unknown          Unknown  Unknown\n",
       "675  Pneumonia  Unknown          Unknown  Unknown\n",
       "676  Pneumonia  Unknown          Unknown  Unknown\n",
       "677  Pneumonia  Unknown          Unknown  Unknown\n",
       "678  Pneumonia  Unknown          Unknown  Unknown\n",
       "\n",
       "[651 rows x 4 columns]"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "findings = dataset.csv[\"finding\"].str.split(\"/\", expand=True)\n",
    "findings.columns = [\"Finding\", \"Type\", \"Genus or Species\", \"Subtype\"]\n",
    "findings = findings.fillna(\"Unknown\")\n",
    "findings = findings[findings.Finding == \"Pneumonia\"]\n",
    "findings"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th>Subtype</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Type</th>\n",
       "      <th>Genus or Species</th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>Aspiration</th>\n",
       "      <th>Unknown</th>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th rowspan=\"9\" valign=\"top\">Bacterial</th>\n",
       "      <th>Chlamydophila</th>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>E.Coli</th>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Klebsiella</th>\n",
       "      <td>9</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Legionella</th>\n",
       "      <td>7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Mycoplasma</th>\n",
       "      <td>5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Nocardia</th>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Staphylococcus</th>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Streptococcus</th>\n",
       "      <td>18</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Unknown</th>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th rowspan=\"2\" valign=\"top\">Fungal</th>\n",
       "      <th>Aspergillosis</th>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Pneumocystis</th>\n",
       "      <td>24</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Lipoid</th>\n",
       "      <th>Unknown</th>\n",
       "      <td>8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Unknown</th>\n",
       "      <th>Unknown</th>\n",
       "      <td>59</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th rowspan=\"6\" valign=\"top\">Viral</th>\n",
       "      <th>COVID-19</th>\n",
       "      <td>468</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Herpes</th>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Influenza</th>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>MERS-CoV</th>\n",
       "      <td>10</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SARS</th>\n",
       "      <td>16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Varicella</th>\n",
       "      <td>5</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                             Subtype\n",
       "Type       Genus or Species         \n",
       "Aspiration Unknown                 1\n",
       "Bacterial  Chlamydophila           1\n",
       "           E.Coli                  4\n",
       "           Klebsiella              9\n",
       "           Legionella              7\n",
       "           Mycoplasma              5\n",
       "           Nocardia                4\n",
       "           Staphylococcus          1\n",
       "           Streptococcus          18\n",
       "           Unknown                 2\n",
       "Fungal     Aspergillosis           2\n",
       "           Pneumocystis           24\n",
       "Lipoid     Unknown                 8\n",
       "Unknown    Unknown                59\n",
       "Viral      COVID-19              468\n",
       "           Herpes                  3\n",
       "           Influenza               4\n",
       "           MERS-CoV               10\n",
       "           SARS                   16\n",
       "           Varicella               5"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "a = findings.groupby([\"Type\", \"Genus or Species\"])[[\"Subtype\"]].count()\n",
    "a"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\\begin{tabular}{llr}\n",
      "\\toprule\n",
      "      &           &  Subtype \\\\\n",
      "Type & Genus or Species &          \\\\\n",
      "\\midrule\n",
      "Aspiration & Unknown &        1 \\\\\n",
      "Bacterial & Chlamydophila &        1 \\\\\n",
      "      & E.Coli &        4 \\\\\n",
      "      & Klebsiella &        9 \\\\\n",
      "      & Legionella &        7 \\\\\n",
      "      & Mycoplasma &        5 \\\\\n",
      "      & Nocardia &        4 \\\\\n",
      "      & Staphylococcus &        1 \\\\\n",
      "      & Streptococcus &       18 \\\\\n",
      "      & Unknown &        2 \\\\\n",
      "Fungal & Aspergillosis &        2 \\\\\n",
      "      & Pneumocystis &       24 \\\\\n",
      "Lipoid & Unknown &        8 \\\\\n",
      "Unknown & Unknown &       59 \\\\\n",
      "Viral & COVID-19 &      468 \\\\\n",
      "      & Herpes  &        3 \\\\\n",
      "      & Influenza &        4 \\\\\n",
      "      & MERS-CoV &       10 \\\\\n",
      "      & SARS &       16 \\\\\n",
      "      & Varicella &        5 \\\\\n",
      "\\bottomrule\n",
      "\\end{tabular}\n",
      "\n"
     ]
    }
   ],
   "source": [
    "print(a.to_latex())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "#dmerge.csv[(dmerge.csv.view == \"L\")]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "dmerge.csv[\"PA/AP\"] = (dmerge.csv.view == \"PA\") | (dmerge.csv.view == \"AP\")\n",
    "dmerge.csv[\"AP Supine\"] = dmerge.csv.view == \"AP Supine\"\n",
    "dmerge.csv[\"L\"] = dmerge.csv.view == \"L\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [],
   "source": [
    "dmerge.csv[\"doicite\"] = \"\\cite{\" + dmerge.csv.doi.replace(\"(\",\"\").replace(\")\",\"\") + \"}\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "df = dmerge.csv.groupby([\"doicite\"])[[\"doi\",\"PA/AP\", \"AP Supine\", \"L\"]].sum()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>PA/AP</th>\n",
       "      <th>AP Supine</th>\n",
       "      <th>L</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>doicite</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>\\cite{10.1007/s00068-020-01364-7}</th>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>\\cite{10.1007/s00270-020-02470-0}</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>\\cite{10.1007/s00296-020-04584-7}</th>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>\\cite{10.1007/s00701-020-04374-x}</th>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>\\cite{10.1007/s11547-020-01200-3}</th>\n",
       "      <td>2</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                   PA/AP  AP Supine  L\n",
       "doicite                                               \n",
       "\\cite{10.1007/s00068-020-01364-7}      3          0  0\n",
       "\\cite{10.1007/s00270-020-02470-0}      1          1  0\n",
       "\\cite{10.1007/s00296-020-04584-7}      3          0  0\n",
       "\\cite{10.1007/s00701-020-04374-x}      0          1  0\n",
       "\\cite{10.1007/s11547-020-01200-3}      2          3  0"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.astype(int).head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array(['PA', 'AP', 'L', 'AP Supine'], dtype=object)"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dmerge.csv.view.unique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
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       "      <td>0</td>\n",
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       "      <th>\\cite{10.1016/j.seizure.2020.04.009}</th>\n",
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       "      <th>\\cite{10.1007/s11547-020-01202-1}</th>\n",
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       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>\\cite{10.1016/j.clim.2020.108450}</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>\\cite{10.1016/S0140-6736(20)30370-6}</th>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>\\cite{10.1016/j.healun.2020.04.004}</th>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>\\cite{10.1016/j.jhin.2020.03.036}</th>\n",
       "      <td>1</td>\n",
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       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>\\cite{10.1093/ageing/afaa068}</th>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <th>\\cite{10.1148/cases.20201394}</th>\n",
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       "    <tr>\n",
       "      <th>\\cite{10.1148/cases.20201558}</th>\n",
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       "    <tr>\n",
       "      <th>\\cite{10.1148/cases.20201559}</th>\n",
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       "    <tr>\n",
       "      <th>\\cite{10.1148/cases.20201815}</th>\n",
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       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>\\cite{10.1148/radiol.2020200269}</th>\n",
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       "      <th>\\cite{10.1148/radiol.2020200274}</th>\n",
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       "      <th>\\cite{10.1148/radiol.2020200490}</th>\n",
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       "    <tr>\n",
       "      <th>\\cite{10.1148/ryct.2020200028}</th>\n",
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       "    <tr>\n",
       "      <th>\\cite{10.1186/s12941-020-00358-y}</th>\n",
       "      <td>1</td>\n",
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       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>\\cite{10.1186/s40779-020-0233-6}</th>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>\\cite{10.11909/j.issn.1671-5411.2020.04.005-0}</th>\n",
       "      <td>1</td>\n",
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       "    <tr>\n",
       "      <th>\\cite{10.3348/kjr.2020.0112}</th>\n",
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       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>\\cite{10.4103/1817-1737.69106}</th>\n",
       "      <td>1</td>\n",
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       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>\\cite{10.4274/balkanmedj.galenos.2020.2020.2.15}</th>\n",
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       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>\\cite{10.7150/thno.46465}</th>\n",
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       "      <th>\\cite{10.7759/cureus.7473}</th>\n",
       "      <td>1</td>\n",
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       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>\\cite{10.1016/j.jiac.2020.03.018}</th>\n",
       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>\\cite{10.1056/NEJMoa2001017}</th>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>\\cite{10.1056/NEJMoa2004500}</th>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>\\cite{10.7759/cureus.7782}</th>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>\\cite{10.1007/s00701-020-04374-x}</th>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>\\cite{10.1016/j.ajem.2020.04.045}</th>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>\\cite{10.1016/j.amjoto.2020.102487}</th>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>\\cite{10.1016/j.bbi.2020.04.077}</th>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>\\cite{10.1016/j.chest.2020.04.024}</th>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>\\cite{10.1016/j.pulmoe.2020.04.012}</th>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>\\cite{10.2214/AJR.20.23034 }</th>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>\\cite{10.2214/AJR.20.23034}</th>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>\\cite{10.7759/cureus.7352}</th>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
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      ],
      "text/plain": [
       "                                                  PA/AP  AP Supine  L\n",
       "doicite                                                              \n",
       "\\cite{10.6084/m9.figshare.12275009}                  48         44  0\n",
       "\\cite{10.1148/rg.242035193}                          11          0  0\n",
       "\\cite{10.1148/radiol.2020201160}                      9          0  0\n",
       "\\cite{10.1148/radiol.2282030593}                      5          0  0\n",
       "\\cite{10.1016/j.jfma.2020.02.007}                     4          0  0\n",
       "\\cite{10.1016/j.jmii.2020.03.008}                     4          0  0\n",
       "\\cite{10.1016/j.radi.2020.04.002}                     4          0  0\n",
       "\\cite{10.1056/NEJMoa2001191}                          4          0  3\n",
       "\\cite{10.1056/nejmc2001272}                           4          0  0\n",
       "\\cite{10.1148/ryct.2020200034}                        4          0  0\n",
       "\\cite{10.1007/s00068-020-01364-7}                     3          0  0\n",
       "\\cite{10.1007/s00296-020-04584-7}                     3          0  0\n",
       "\\cite{10.1016/j.anl.2020.04.002}                      3          0  0\n",
       "\\cite{10.1016/j.chom.2020.03.021}                     3          0  0\n",
       "\\cite{10.1016/j.idcr.2020.e00775}                     3          0  0\n",
       "\\cite{10.1016/j.medcle.2020.03.004}                   3          0  0\n",
       "\\cite{10.1093/cid/ciaa199}                            3          0  0\n",
       "\\cite{10.1148/ryct.2020200033}                        3          0  0\n",
       "\\cite{10.3346/jkms.2020.35.e79}                       3          0  0\n",
       "\\cite{10.3348/kjr.2020.0132}                          3          0  0\n",
       "\\cite{10.4269/ajtmh.20-0203}                          3          0  0\n",
       "\\cite{10.1007/s11547-020-01200-3}                     2          3  0\n",
       "\\cite{10.1111/all.14238}                              2          3  0\n",
       "\\cite{10.1016/j.idcr.2020.e00762}                     2          1  0\n",
       "\\cite{10.1016/S0140-6736(20)30211-7}                  2          0  0\n",
       "\\cite{10.1016/S1473-3099(20)30111-0}                  2          0  0\n",
       "\\cite{10.1016/j.cardfail.2020.04.007}                 2          0  0\n",
       "\\cite{10.1016/j.crad.2020.04.002}                     2          0  0\n",
       "\\cite{10.1016/j.jmii.2020.02.009}                     2          0  0\n",
       "\\cite{10.1016/j.jmii.2020.03.003}                     2          0  0\n",
       "\\cite{10.1016/j.kint.2020.03.018}                     2          0  0\n",
       "\\cite{10.1016/j.seizure.2020.04.009}                  2          0  0\n",
       "\\cite{10.1038/s41379-020-0536-x}                      2          0  0\n",
       "\\cite{10.1038/s41591-020-0819-2}                      2          0  0\n",
       "\\cite{10.1056/NEJMc2001573}                           2          0  0\n",
       "\\cite{10.11909/j.issn.1671-5411.2020.04.005}          2          0  0\n",
       "\\cite{10.7759/cureus.7482}                            2          0  0\n",
       "\\cite{10.1007/s11547-020-01203-0}                     1          7  0\n",
       "\\cite{10.1016/j.hrcr.2020.04.015}                     1          3  0\n",
       "\\cite{10.1016/S2213-2600(20)30076-X}                  1          2  0\n",
       "\\cite{10.1016/j.jgar.2020.04.024}                     1          2  0\n",
       "\\cite{10.1007/s00270-020-02470-0}                     1          1  0\n",
       "\\cite{10.1007/s11547-020-01202-1}                     1          1  0\n",
       "\\cite{10.1016/j.clim.2020.108450}                     1          1  0\n",
       "\\cite{10.1016/S0140-6736(20)30370-6}                  1          0  0\n",
       "\\cite{10.1016/j.healun.2020.04.004}                   1          0  0\n",
       "\\cite{10.1016/j.jhin.2020.03.036}                     1          0  0\n",
       "\\cite{10.1093/ageing/afaa068}                         1          0  0\n",
       "\\cite{10.1148/cases.20201394}                         1          0  0\n",
       "\\cite{10.1148/cases.20201558}                         1          0  0\n",
       "\\cite{10.1148/cases.20201559}                         1          0  0\n",
       "\\cite{10.1148/cases.20201815}                         1          0  0\n",
       "\\cite{10.1148/radiol.2020200269}                      1          0  0\n",
       "\\cite{10.1148/radiol.2020200274}                      1          0  0\n",
       "\\cite{10.1148/radiol.2020200490}                      1          0  0\n",
       "\\cite{10.1148/ryct.2020200028}                        1          0  0\n",
       "\\cite{10.1186/s12941-020-00358-y}                     1          0  0\n",
       "\\cite{10.1186/s40779-020-0233-6}                      1          0  0\n",
       "\\cite{10.11909/j.issn.1671-5411.2020.04.005-0}        1          0  0\n",
       "\\cite{10.3348/kjr.2020.0112}                          1          0  0\n",
       "\\cite{10.4103/1817-1737.69106}                        1          0  0\n",
       "\\cite{10.4274/balkanmedj.galenos.2020.2020.2.15}      1          0  0\n",
       "\\cite{10.7150/thno.46465}                             1          0  0\n",
       "\\cite{10.7759/cureus.7473}                            1          0  0\n",
       "\\cite{10.1016/j.jiac.2020.03.018}                     0          5  0\n",
       "\\cite{10.1056/NEJMoa2001017}                          0          2  0\n",
       "\\cite{10.1056/NEJMoa2004500}                          0          2  0\n",
       "\\cite{10.7759/cureus.7782}                            0          2  0\n",
       "\\cite{10.1007/s00701-020-04374-x}                     0          1  0\n",
       "\\cite{10.1016/j.ajem.2020.04.045}                     0          1  0\n",
       "\\cite{10.1016/j.amjoto.2020.102487}                   0          1  0\n",
       "\\cite{10.1016/j.bbi.2020.04.077}                      0          1  0\n",
       "\\cite{10.1016/j.chest.2020.04.024}                    0          1  0\n",
       "\\cite{10.1016/j.pulmoe.2020.04.012}                   0          1  0\n",
       "\\cite{10.2214/AJR.20.23034 }                          0          1  0\n",
       "\\cite{10.2214/AJR.20.23034}                           0          1  0\n",
       "\\cite{10.7759/cureus.7352}                            0          1  0"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "with pd.option_context('display.max_rows', 10000, 'display.max_columns', 10000):\n",
    "    display(df.astype(int).sort_values([\"PA/AP\",\"AP Supine\"], ascending=False))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\\begin{tabular}{lrrr}\n",
      "\\toprule\n",
      "{} &  PA/AP &  AP Supine &  L \\\\\n",
      "doicite                                          &        &            &    \\\\\n",
      "\\midrule\n",
      "\\cite{10.6084/m9.figshare.12275009}              &     48 &         44 &  0 \\\\\n",
      "\\cite{10.1148/rg.242035193}                      &     11 &          0 &  0 \\\\\n",
      "\\cite{10.1148/radiol.2020201160}                 &      9 &          0 &  0 \\\\\n",
      "\\cite{10.1148/radiol.2282030593}                 &      5 &          0 &  0 \\\\\n",
      "\\cite{10.1016/j.jfma.2020.02.007}                &      4 &          0 &  0 \\\\\n",
      "\\cite{10.1016/j.jmii.2020.03.008}                &      4 &          0 &  0 \\\\\n",
      "\\cite{10.1016/j.radi.2020.04.002}                &      4 &          0 &  0 \\\\\n",
      "\\cite{10.1056/NEJMoa2001191}                     &      4 &          0 &  3 \\\\\n",
      "\\cite{10.1056/nejmc2001272}                      &      4 &          0 &  0 \\\\\n",
      "\\cite{10.1148/ryct.2020200034}                   &      4 &          0 &  0 \\\\\n",
      "\\cite{10.1007/s00068-020-01364-7}                &      3 &          0 &  0 \\\\\n",
      "\\cite{10.1007/s00296-020-04584-7}                &      3 &          0 &  0 \\\\\n",
      "\\cite{10.1016/j.anl.2020.04.002}                 &      3 &          0 &  0 \\\\\n",
      "\\cite{10.1016/j.chom.2020.03.021}                &      3 &          0 &  0 \\\\\n",
      "\\cite{10.1016/j.idcr.2020.e00775}                &      3 &          0 &  0 \\\\\n",
      "\\cite{10.1016/j.medcle.2020.03.004}              &      3 &          0 &  0 \\\\\n",
      "\\cite{10.1093/cid/ciaa199}                       &      3 &          0 &  0 \\\\\n",
      "\\cite{10.1148/ryct.2020200033}                   &      3 &          0 &  0 \\\\\n",
      "\\cite{10.3346/jkms.2020.35.e79}                  &      3 &          0 &  0 \\\\\n",
      "\\cite{10.3348/kjr.2020.0132}                     &      3 &          0 &  0 \\\\\n",
      "\\cite{10.4269/ajtmh.20-0203}                     &      3 &          0 &  0 \\\\\n",
      "\\cite{10.1007/s11547-020-01200-3}                &      2 &          3 &  0 \\\\\n",
      "\\cite{10.1111/all.14238}                         &      2 &          3 &  0 \\\\\n",
      "\\cite{10.1016/j.idcr.2020.e00762}                &      2 &          1 &  0 \\\\\n",
      "\\cite{10.1016/S0140-6736(20)30211-7}             &      2 &          0 &  0 \\\\\n",
      "\\cite{10.1016/S1473-3099(20)30111-0}             &      2 &          0 &  0 \\\\\n",
      "\\cite{10.1016/j.cardfail.2020.04.007}            &      2 &          0 &  0 \\\\\n",
      "\\cite{10.1016/j.crad.2020.04.002}                &      2 &          0 &  0 \\\\\n",
      "\\cite{10.1016/j.jmii.2020.02.009}                &      2 &          0 &  0 \\\\\n",
      "\\cite{10.1016/j.jmii.2020.03.003}                &      2 &          0 &  0 \\\\\n",
      "\\cite{10.1016/j.kint.2020.03.018}                &      2 &          0 &  0 \\\\\n",
      "\\cite{10.1016/j.seizure.2020.04.009}             &      2 &          0 &  0 \\\\\n",
      "\\cite{10.1038/s41379-020-0536-x}                 &      2 &          0 &  0 \\\\\n",
      "\\cite{10.1038/s41591-020-0819-2}                 &      2 &          0 &  0 \\\\\n",
      "\\cite{10.1056/NEJMc2001573}                      &      2 &          0 &  0 \\\\\n",
      "\\cite{10.11909/j.issn.1671-5411.2020.04.005}     &      2 &          0 &  0 \\\\\n",
      "\\cite{10.7759/cureus.7482}                       &      2 &          0 &  0 \\\\\n",
      "\\cite{10.1007/s11547-020-01203-0}                &      1 &          7 &  0 \\\\\n",
      "\\cite{10.1016/j.hrcr.2020.04.015}                &      1 &          3 &  0 \\\\\n",
      "\\cite{10.1016/S2213-2600(20)30076-X}             &      1 &          2 &  0 \\\\\n",
      "\\cite{10.1016/j.jgar.2020.04.024}                &      1 &          2 &  0 \\\\\n",
      "\\cite{10.1007/s00270-020-02470-0}                &      1 &          1 &  0 \\\\\n",
      "\\cite{10.1007/s11547-020-01202-1}                &      1 &          1 &  0 \\\\\n",
      "\\cite{10.1016/j.clim.2020.108450}                &      1 &          1 &  0 \\\\\n",
      "\\cite{10.1016/S0140-6736(20)30370-6}             &      1 &          0 &  0 \\\\\n",
      "\\cite{10.1016/j.healun.2020.04.004}              &      1 &          0 &  0 \\\\\n",
      "\\cite{10.1016/j.jhin.2020.03.036}                &      1 &          0 &  0 \\\\\n",
      "\\cite{10.1093/ageing/afaa068}                    &      1 &          0 &  0 \\\\\n",
      "\\cite{10.1148/cases.20201394}                    &      1 &          0 &  0 \\\\\n",
      "\\cite{10.1148/cases.20201558}                    &      1 &          0 &  0 \\\\\n",
      "\\cite{10.1148/cases.20201559}                    &      1 &          0 &  0 \\\\\n",
      "\\cite{10.1148/cases.20201815}                    &      1 &          0 &  0 \\\\\n",
      "\\cite{10.1148/radiol.2020200269}                 &      1 &          0 &  0 \\\\\n",
      "\\cite{10.1148/radiol.2020200274}                 &      1 &          0 &  0 \\\\\n",
      "\\cite{10.1148/radiol.2020200490}                 &      1 &          0 &  0 \\\\\n",
      "\\cite{10.1148/ryct.2020200028}                   &      1 &          0 &  0 \\\\\n",
      "\\cite{10.1186/s12941-020-00358-y}                &      1 &          0 &  0 \\\\\n",
      "\\cite{10.1186/s40779-020-0233-6}                 &      1 &          0 &  0 \\\\\n",
      "\\cite{10.11909/j.issn.1671-5411.2020.04.005-0}   &      1 &          0 &  0 \\\\\n",
      "\\cite{10.3348/kjr.2020.0112}                     &      1 &          0 &  0 \\\\\n",
      "\\cite{10.4103/1817-1737.69106}                   &      1 &          0 &  0 \\\\\n",
      "\\cite{10.4274/balkanmedj.galenos.2020.2020.2.15} &      1 &          0 &  0 \\\\\n",
      "\\cite{10.7150/thno.46465}                        &      1 &          0 &  0 \\\\\n",
      "\\cite{10.7759/cureus.7473}                       &      1 &          0 &  0 \\\\\n",
      "\\cite{10.1016/j.jiac.2020.03.018}                &      0 &          5 &  0 \\\\\n",
      "\\cite{10.1056/NEJMoa2001017}                     &      0 &          2 &  0 \\\\\n",
      "\\cite{10.1056/NEJMoa2004500}                     &      0 &          2 &  0 \\\\\n",
      "\\cite{10.7759/cureus.7782}                       &      0 &          2 &  0 \\\\\n",
      "\\cite{10.1007/s00701-020-04374-x}                &      0 &          1 &  0 \\\\\n",
      "\\cite{10.1016/j.ajem.2020.04.045}                &      0 &          1 &  0 \\\\\n",
      "\\cite{10.1016/j.amjoto.2020.102487}              &      0 &          1 &  0 \\\\\n",
      "\\cite{10.1016/j.bbi.2020.04.077}                 &      0 &          1 &  0 \\\\\n",
      "\\cite{10.1016/j.chest.2020.04.024}               &      0 &          1 &  0 \\\\\n",
      "\\cite{10.1016/j.pulmoe.2020.04.012}              &      0 &          1 &  0 \\\\\n",
      "\\cite{10.2214/AJR.20.23034 }                     &      0 &          1 &  0 \\\\\n",
      "\\cite{10.2214/AJR.20.23034}                      &      0 &          1 &  0 \\\\\n",
      "\\cite{10.7759/cureus.7352}                       &      0 &          1 &  0 \\\\\n",
      "\\bottomrule\n",
      "\\end{tabular}\n",
      "\n"
     ]
    }
   ],
   "source": [
    "print(df.astype(int).sort_values([\"PA/AP\",\"AP Supine\"], ascending=False).to_latex(escape=False))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "df[\"PA\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [],
   "source": [
    "alreadyhave = pd.read_csv(\"alreadyhave.txt\",header=None)[0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 71,
   "metadata": {},
   "outputs": [],
   "source": [
    "import doi2bib, doi2bib.crossref"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 136,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 179,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0            10.1056/nejmc2001272\n",
       "1            10.1056/NEJMc2001573\n",
       "2     10.1016/S0140-67362030211-7\n",
       "3            10.1148/rg.242035193\n",
       "4     10.1016/S0140-67362030370-6\n",
       "5       10.1148/radiol.2020200269\n",
       "6           10.1056/NEJMoa2001191\n",
       "7         10.1148/ryct.2020200034\n",
       "8         10.1148/ryct.2020200028\n",
       "9        10.3346/jkms.2020.35.e79\n",
       "10      10.1148/radiol.2020200490\n",
       "11     10.1016/j.jfma.2020.02.007\n",
       "12              10.1111/all.14238\n",
       "13     10.1016/j.jmii.2020.03.003\n",
       "14            10.1093/cid/ciaa199\n",
       "15          10.3348/kjr.2020.0132\n",
       "16     10.1016/j.jmii.2020.03.008\n",
       "17    10.1016/S1473-30992030111-0\n",
       "18      10.1038/s41591-020-0819-2\n",
       "19          10.3348/kjr.2020.0112\n",
       "20         10.1148/cases.20201558\n",
       "21        10.4103/1817-1737.69106\n",
       "22         10.1148/cases.20201815\n",
       "23         10.1148/cases.20201559\n",
       "24         10.1148/cases.20201394\n",
       "25      10.1148/radiol.2020201160\n",
       "26        10.1148/ryct.2020200033\n",
       "27      10.1148/radiol.2020200274\n",
       "28      10.1148/radiol.2282030593\n",
       "29           10.2214/AJR.20.23034\n",
       "30    10.1016/S2213-26002030076-X\n",
       "31          10.4269/ajtmh.20-0203\n",
       "Name: 0, dtype: object"
      ]
     },
     "execution_count": 179,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "alreadyhave"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 138,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pybtex.database.input import bibtex\n",
    "import pybtex.database.output.bibtex"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 178,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "@article{10.1016/s0140-67362030211-7,\n",
      "    author = \"Chen, Nanshan and Zhou, Min and Dong, Xuan and Qu, Jieming and Gong, Fengyun and Han, Yang and Qiu, Yang and Wang, Jingli and Liu, Ying and Wei, Yuan and Xia, Jia{\\textquotesingle}an and Yu, Ting and Zhang, Xinxin and Zhang, Li\",\n",
      "    doi = \"10.1016/s0140-6736(20)30211-7\",\n",
      "    year = \"2020\",\n",
      "    title = \"Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study\",\n",
      "    journal = \"The Lancet\"\n",
      "}\n",
      "@article{10.1016/s0140-67362030370-6,\n",
      "    author = \"Silverstein, William Kyle and Stroud, Lynfa and Cleghorn, Graham Edward and Leis, Jerome Allen\",\n",
      "    doi = \"10.1016/s0140-6736(20)30370-6\",\n",
      "    year = \"2020\",\n",
      "    title = \"First imported case of 2019 novel coronavirus in Canada, presenting as mild pneumonia\",\n",
      "    journal = \"The Lancet\"\n",
      "}\n",
      "@article{10.1016/s1473-30992030111-0,\n",
      "    author = \"Cuong, Le Van and Giang, Hoang Thi Nam and Linh, Le Khac and Shah, Jaffer and Sy, Le Van and Hung, Trinh Huu and Reda, Abdullah and Truong, Luong Ngoc and Tien, Do Xuan and Huy, Nguyen Tien\",\n",
      "    doi = \"10.1016/s1473-3099(20)30111-0\",\n",
      "    year = \"2020\",\n",
      "    title = \"The first Vietnamese case of COVID-19 acquired from China\",\n",
      "    journal = \"The Lancet Infectious Diseases\"\n",
      "}\n",
      "@article{10.2214/ajr.20.23034,\n",
      "    author = \"Salehi, Sana and Abedi, Aidin and Balakrishnan, Sudheer and Gholamrezanezhad, Ali\",\n",
      "    doi = \"10.2214/ajr.20.23034\",\n",
      "    year = \"2020\",\n",
      "    title = \"Coronavirus Disease 2019 (COVID-19): A Systematic Review of Imaging Findings in 919 Patients\",\n",
      "    journal = \"American Journal of Roentgenology\"\n",
      "}\n",
      "@article{10.1016/s2213-26002030076-x,\n",
      "    author = \"Xu, Zhe and Shi, Lei and Wang, Yijin and Zhang, Jiyuan and Huang, Lei and Zhang, Chao and Liu, Shuhong and Zhao, Peng and Liu, Hongxia and Zhu, Li and Tai, Yanhong and Bai, Changqing and Gao, Tingting and Song, Jinwen and Xia, Peng and Dong, Jinghui and Zhao, Jingmin and Wang, Fu-Sheng\",\n",
      "    doi = \"10.1016/s2213-2600(20)30076-x\",\n",
      "    year = \"2020\",\n",
      "    title = \"Pathological findings of COVID-19 associated with acute respiratory distress syndrome\",\n",
      "    journal = \"The Lancet Respiratory Medicine\"\n",
      "}\n",
      "@article{10.1056/nejmoa2001017,\n",
      "    author = \"Zhu, Na and Zhang, Dingyu and Wang, Wenling and Li, Xingwang and Yang, Bo and Song, Jingdong and Zhao, Xiang and Huang, Baoying and Shi, Weifeng and Lu, Roujian and Niu, Peihua and Zhan, Faxian and Ma, Xuejun and Wang, Dayan and Xu, Wenbo and Wu, Guizhen and Gao, George F. and Tan, Wenjie\",\n",
      "    doi = \"10.1056/nejmoa2001017\",\n",
      "    year = \"2020\",\n",
      "    title = \"A Novel Coronavirus from Patients with Pneumonia in China, 2019\",\n",
      "    journal = \"New England Journal of Medicine\"\n",
      "}\n",
      "@article{10.1007/s00068-020-01364-7,\n",
      "    author = \"Coimbra, Raul and Edwards, Sara and Kurihara, Hayato and Bass, Gary Alan and Balogh, Zsolt J. and Tilsed, Jonathan and Faccincani, Roberto and Carlucci, Michele and Casas, Isidro Mart{\\'{\\i}}nez and Gaarder, Christine and Tabuenca, Arnold and Coimbra, Bruno C. and Marzi, Ingo\",\n",
      "    doi = \"10.1007/s00068-020-01364-7\",\n",
      "    year = \"2020\",\n",
      "    title = \"European Society of Trauma and Emergency Surgery (ESTES) recommendations for trauma and emergency surgery preparation during times of COVID-19 infection\",\n",
      "    journal = \"European Journal of Trauma and Emergency Surgery\"\n",
      "}\n",
      "@article{10.1007/s00270-020-02470-0,\n",
      "    author = \"Monfardini, Lorenzo and Sallemi, Claudio and Gennaro, Nicol{\\`{o}} and Pedicini, Vittorio and Bn{\\`{a}}, Claudio\",\n",
      "    doi = \"10.1007/s00270-020-02470-0\",\n",
      "    year = \"2020\",\n",
      "    title = \"Contribution of Interventional Radiology to the Management of COVID-19 patient\",\n",
      "    journal = \"{CardioVascular} and Interventional Radiology\"\n",
      "}\n",
      "@article{10.1007/s00296-020-04584-7,\n",
      "    author = \"Song, Jehun and Kang, Seongmin and Choi, Seung Won and Seo, Kwang Won and Lee, Sunggun and So, Min Wook and Lim, Doo-Ho\",\n",
      "    doi = \"10.1007/s00296-020-04584-7\",\n",
      "    year = \"2020\",\n",
      "    title = \"Coronavirus Disease 19 (COVID-19) complicated with pneumonia in a patient with rheumatoid arthritis receiving conventional disease-modifying antirheumatic drugs\",\n",
      "    journal = \"Rheumatology International\"\n",
      "}\n",
      "@article{10.1007/s00701-020-04374-x,\n",
      "    author = \"Zanin, Luca and Saraceno, Giorgio and Panciani, Pier Paolo and Renisi, Giulia and Signorini, Liana and Migliorati, Karol and Fontanella, Marco Maria\",\n",
      "    doi = \"10.1007/s00701-020-04374-x\",\n",
      "    year = \"2020\",\n",
      "    title = \"SARS-CoV-2 can induce brain and spine demyelinating lesions\",\n",
      "    journal = \"Acta Neurochirurgica\"\n",
      "}\n",
      "@article{10.1056/nejmoa2004500,\n",
      "    author = \"Bhatraju, Pavan K. and Ghassemieh, Bijan J. and Nichols, Michelle and Kim, Richard and Jerome, Keith R. and Nalla, Arun K. and Greninger, Alexander L. and Pipavath, Sudhakar and Wurfel, Mark M. and Evans, Laura and Kritek, Patricia A. and West, T. Eoin and Luks, Andrew and Gerbino, Anthony and Dale, Chris R. and Goldman, Jason D. and O'Mahony, Shane and Mikacenic, Carmen\",\n",
      "    doi = \"10.1056/nejmoa2004500\",\n",
      "    year = \"2020\",\n",
      "    title = \"Covid-19 in Critically Ill Patients in the Seattle Region \\textemdash Case Series\",\n",
      "    journal = \"New England Journal of Medicine\"\n",
      "}\n",
      "@article{10.1007/s11547-020-01200-3,\n",
      "    author = \"Borghesi, Andrea and Maroldi, Roberto\",\n",
      "    doi = \"10.1007/s11547-020-01200-3\",\n",
      "    year = \"2020\",\n",
      "    title = \"COVID-19 outbreak in Italy: experimental chest X-ray scoring system for quantifying and monitoring disease progression\",\n",
      "    journal = \"La radiologia medica\"\n",
      "}\n",
      "@article{10.1007/s11547-020-01202-1,\n",
      "    author = \"Borghesi, Andrea and Zigliani, Angelo and Masciullo, Roberto and Golemi, Salvatore and Maculotti, Patrizia and Farina, Davide and Maroldi, Roberto\",\n",
      "    doi = \"10.1007/s11547-020-01202-1\",\n",
      "    year = \"2020\",\n",
      "    title = \"Radiographic severity index in COVID-19 pneumonia: relationship to age and sex in 783 Italian patients\",\n",
      "    journal = \"La radiologia medica\"\n",
      "}\n",
      "@article{10.1007/s11547-020-01203-0,\n",
      "    author = \"Fichera, Giulia and Stramare, Roberto and Conti, Giorgio De and Motta, Raffaella and Giraudo, Chiara\",\n",
      "    doi = \"10.1007/s11547-020-01203-0\",\n",
      "    year = \"2020\",\n",
      "    title = \"It's not over until it's over: the chameleonic behavior of COVID-19 over a six-day period\",\n",
      "    journal = \"La radiologia medica\"\n",
      "}\n",
      "@article{10.1016/j.ajem.2020.04.045,\n",
      "    author = \"Prince, Garrett and Sergel, Michelle\",\n",
      "    doi = \"10.1016/j.ajem.2020.04.045\",\n",
      "    year = \"2020\",\n",
      "    title = \"Persistent hiccups as an atypical presenting complaint of COVID-19\",\n",
      "    journal = \"The American Journal of Emergency Medicine\"\n",
      "}\n",
      "@article{10.1016/j.amjoto.2020.102487,\n",
      "    author = \"Fidan, Vural\",\n",
      "    doi = \"10.1016/j.amjoto.2020.102487\",\n",
      "    year = \"2020\",\n",
      "    title = \"New type of corona virus induced acute otitis media in adult\",\n",
      "    journal = \"American Journal of Otolaryngology\"\n",
      "}\n",
      "@article{10.1016/j.anl.2020.04.002,\n",
      "    author = \"Hiramatsu, Mariko and Nishio, Naoki and Ozaki, Masayuki and Shindo, Yuichiro and Suzuki, Katsunao and Yamamoto, Takanori and Fujimoto, Yasushi and Sone, Michihiko\",\n",
      "    doi = \"10.1016/j.anl.2020.04.002\",\n",
      "    year = \"2020\",\n",
      "    title = \"Anesthetic and surgical management of tracheostomy in a patient with COVID-19\",\n",
      "    journal = \"Auris Nasus Larynx\"\n",
      "}\n",
      "@article{10.1016/j.bbi.2020.04.077,\n",
      "    author = \"Avula, Akshay and Nalleballe, Krishna and Narula, Naureen and Sapozhnikov, Steven and Dandu, Vasuki and Toom, Sudhamshi and Glaser, Allison and Elsayegh, Dany\",\n",
      "    doi = \"10.1016/j.bbi.2020.04.077\",\n",
      "    year = \"2020\",\n",
      "    title = \"COVID-19 presenting as stroke\",\n",
      "    journal = \"Brain, Behavior, and Immunity\"\n",
      "}\n",
      "@article{10.1016/j.cardfail.2020.04.007,\n",
      "    author = \"SINGH, RAJAT and DOMENICO, CHRISTOPHER and RAO, SRIRAM D. and URGO, KIMBERLY and PRENNER, STUART B. and WALD, JOYCE W. and ATLURI, PAVAN and BIRATI, EDO Y.\",\n",
      "    doi = \"10.1016/j.cardfail.2020.04.007\",\n",
      "    year = \"2020\",\n",
      "    title = \"Novel Coronavirus Disease 2019 in a Patient on Durable Left Ventricular Assist Device Support\",\n",
      "    journal = \"Journal of Cardiac Failure\"\n",
      "}\n",
      "@article{10.1016/j.chest.2020.04.024,\n",
      "    author = \"Radbel, Jared and Narayanan, Navaneeth and Bhatt, Pinki J.\",\n",
      "    doi = \"10.1016/j.chest.2020.04.024\",\n",
      "    year = \"2020\",\n",
      "    title = \"Use of Tocilizumab for COVID-19-Induced Cytokine Release Syndrome\",\n",
      "    journal = \"Chest\"\n",
      "}\n",
      "@article{10.1016/j.chom.2020.03.021,\n",
      "    author = \"Ong, Eugenia Ziying and Chan, Yvonne Fu Zi and Leong, Wan Ying and Lee, Natalie Mei Ying and Kalimuddin, Shirin and Mohideen, Salahudeen Mohamed Haja and Chan, Kian Sing and Tan, Anthony Tanoto and Bertoletti, Antonio and Ooi, Eng Eong and Low, Jenny Guek Hong\",\n",
      "    doi = \"10.1016/j.chom.2020.03.021\",\n",
      "    year = \"2020\",\n",
      "    title = \"A Dynamic Immune Response Shapes COVID-19 Progression\",\n",
      "    journal = \"Cell Host {\\\\&} Microbe\"\n",
      "}\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "@article{10.1016/j.clim.2020.108450,\n",
      "    author = \"Mastaglio, Sara and Ruggeri, Annalisa and Risitano, Antonio M. and Angelillo, Piera and Yancopoulou, Despina and Mastellos, Dimitrios C. and Huber-Lang, Markus and Piemontese, Simona and Assanelli, Andrea and Garlanda, Cecilia and Lambris, John D. and Ciceri, Fabio\",\n",
      "    doi = \"10.1016/j.clim.2020.108450\",\n",
      "    year = \"2020\",\n",
      "    title = \"The first case of COVID-19 treated with the complement C3 inhibitor AMY-101\",\n",
      "    journal = \"Clinical Immunology\"\n",
      "}\n",
      "@article{10.1016/j.crad.2020.04.002,\n",
      "    author = \"Hare, S.S. and Rodrigues, J.C.L. and Nair, A. and Jacob, J. and Upile, S. and Johnstone, A. and Mcstay, R. and Edey, A. and Robinson, G.\",\n",
      "    doi = \"10.1016/j.crad.2020.04.002\",\n",
      "    year = \"2020\",\n",
      "    title = \"The continuing evolution of COVID-19 imaging pathways in the UK: a British Society of Thoracic Imaging expert reference group update\",\n",
      "    journal = \"Clinical Radiology\"\n",
      "}\n",
      "@article{10.1016/j.healun.2020.04.004,\n",
      "    author = \"Aigner, Clemens and Dittmer, Ulf and Kamler, Markus and Collaud, Stephane and Taube, Christian\",\n",
      "    doi = \"10.1016/j.healun.2020.04.004\",\n",
      "    year = \"2020\",\n",
      "    title = \"COVID-19 in a lung transplant recipient\",\n",
      "    journal = \"The Journal of Heart and Lung Transplantation\"\n",
      "}\n",
      "@article{10.1016/j.hrcr.2020.04.015,\n",
      "    author = \"Ebrille, Elisa and Lucciola, Maria Teresa and Amellone, Claudia and Ballocca, Flavia and Orlando, Fabrizio and Giammaria, Massimo\",\n",
      "    doi = \"10.1016/j.hrcr.2020.04.015\",\n",
      "    year = \"2020\",\n",
      "    title = \"Syncope as the presenting symptom of COVID-19 infection\",\n",
      "    journal = \"{HeartRhythm} Case Reports\"\n",
      "}\n",
      "@article{10.1016/j.jgar.2020.04.024,\n",
      "    author = \"Dastan, Farzaneh and Saffaei, Ali and Mortazavi, Seyed Mehdi and Jamaati, Hamidreza and Adnani, Nadia and Roudi, Sasan Samiee and Kiani, Arda and Abedini, Atefeh and Hashemian, Seyed MohammadReza\",\n",
      "    doi = \"10.1016/j.jgar.2020.04.024\",\n",
      "    year = \"2020\",\n",
      "    title = \"Continues renal replacement therapy (CRRT) with disposable hemoperfusion cartridge: A promising option for severe COVID-19\",\n",
      "    journal = \"Journal of Global Antimicrobial Resistance\"\n",
      "}\n",
      "@article{10.1016/j.jhin.2020.03.036,\n",
      "    author = \"Wong, S.C.Y. and Kwong, R.T-S. and Wu, T.C. and Chan, J.W.M. and Chu, M.Y. and Lee, S.Y. and Wong, H.Y. and Lung, D.C.\",\n",
      "    doi = \"10.1016/j.jhin.2020.03.036\",\n",
      "    year = \"2020\",\n",
      "    title = \"Risk of nosocomial transmission of coronavirus disease 2019: an experience in a general ward setting in Hong Kong\",\n",
      "    journal = \"Journal of Hospital Infection\"\n",
      "}\n",
      "@article{10.1016/j.jiac.2020.03.018,\n",
      "    author = \"Nakamura, Kazuha and Hikone, Mayu and Shimizu, Hiroshi and Kuwahara, Yusuke and Tanabe, Maki and Kobayashi, Mioko and Ishida, Takuto and Sugiyama, Kazuhiro and Washino, Takuya and Sakamoto, Naoya and Hamabe, Yuichi\",\n",
      "    doi = \"10.1016/j.jiac.2020.03.018\",\n",
      "    year = \"2020\",\n",
      "    title = \"A sporadic COVID-19 pneumonia treated with extracorporeal membrane oxygenation in Tokyo, Japan: A case report\",\n",
      "    journal = \"Journal of Infection and Chemotherapy\"\n",
      "}\n",
      "@article{10.1016/j.jmii.2020.02.009,\n",
      "    author = \"Huang, Wei-Hsuan and Teng, Ling-Chiao and Yeh, Ting-Kuang and Chen, Yu-Jen and Lo, Wei-Jung and Wu, Ming-Ju and Chin, Chun-Shih and Tsan, Yu-Tse and Lin, Tzu-Chieh and Chai, Jyh-Wen and Lin, Chin-Fu and Tseng, Chien-Hao and Liu, Chia-Wei and Wu, Chi-Mei and Chen, Po-Yen and Shi, Zhi-Yuan and Liu, Po-Yu\",\n",
      "    doi = \"10.1016/j.jmii.2020.02.009\",\n",
      "    year = \"2020\",\n",
      "    title = \"2019 novel coronavirus disease (COVID-19) in Taiwan: Reports of two cases from Wuhan, China\",\n",
      "    journal = \"Journal of Microbiology, Immunology and Infection\"\n",
      "}\n",
      "@article{10.1016/j.kint.2020.03.018,\n",
      "    author = \"Banerjee, Debasish and Popoola, Joyce and Shah, Sapna and Ster, Irina Chis and Quan, Virginia and Phanish, Mysore\",\n",
      "    doi = \"10.1016/j.kint.2020.03.018\",\n",
      "    year = \"2020\",\n",
      "    title = \"COVID-19 infection in kidney transplant recipients\",\n",
      "    journal = \"Kidney International\"\n",
      "}\n",
      "@article{10.1016/j.medcle.2020.03.004,\n",
      "    author = \"S{\\'{a}}nchez-Oro, Raquel and Nuez, Julio Torres and Mart{\\'{\\i}}nez-Sanz, Gloria\",\n",
      "    doi = \"10.1016/j.medcle.2020.03.004\",\n",
      "    year = \"2020\",\n",
      "    title = \"Radiological findings for diagnosis of SARS-CoV-2 pneumonia (COVID-19)\",\n",
      "    journal = \"Medicina Cl{\\'{\\i}}nica (English Edition)\"\n",
      "}\n",
      "@article{10.1016/j.pulmoe.2020.04.012,\n",
      "    author = \"Tonelli, R. and Iattoni, A. and Girardis, M. and Pietri, L. De and Clini, E. and Mussini, C.\",\n",
      "    doi = \"10.1016/j.pulmoe.2020.04.012\",\n",
      "    year = \"2020\",\n",
      "    title = \"Never Give Up: Lesson learned from a severe COVID-19 patient\",\n",
      "    journal = \"Pulmonology\"\n",
      "}\n",
      "@article{10.1016/j.radi.2020.04.002,\n",
      "    author = \"Woznitza, N. and Nair, A. and Hare, S.S.\",\n",
      "    doi = \"10.1016/j.radi.2020.04.002\",\n",
      "    year = \"2020\",\n",
      "    title = \"COVID-19: A case series to support radiographer preliminary clinical evaluation\",\n",
      "    journal = \"Radiography\"\n",
      "}\n",
      "@article{10.1016/j.seizure.2020.04.009,\n",
      "    author = \"Vollono, Catello and Rollo, Eleonora and Romozzi, Marina and Frisullo, Giovanni and Servidei, Serenella and Borghetti, Alberto and Calabresi, Paolo\",\n",
      "    doi = \"10.1016/j.seizure.2020.04.009\",\n",
      "    year = \"2020\",\n",
      "    title = \"Focal status epilepticus as unique clinical feature of COVID-19: A case report\",\n",
      "    journal = \"Seizure\"\n",
      "}\n",
      "@article{10.1038/s41379-020-0536-x,\n",
      "    author = \"Tian, Sufang and Xiong, Yong and Liu, Huan and Niu, Li and Guo, Jianchun and Liao, Meiyan and Xiao, Shu-Yuan\",\n",
      "    doi = \"10.1038/s41379-020-0536-x\",\n",
      "    year = \"2020\",\n",
      "    title = \"Pathological study of the 2019 novel coronavirus disease (COVID-19) through postmortem core biopsies\",\n",
      "    journal = \"Modern Pathology\"\n",
      "}\n",
      "@article{10.1093/ageing/afaa068,\n",
      "    author = \"Tay, Hui Sian and Harwood, Rowan\",\n",
      "    doi = \"10.1093/ageing/afaa068\",\n",
      "    year = \"2020\",\n",
      "    title = \"Atypical presentation of COVID-19 in a frail older person\",\n",
      "    journal = \"Age and Ageing\"\n",
      "}\n",
      "@article{10.1186/s12941-020-00358-y,\n",
      "    author = \"Mill{\\'{a}}n-O{\\\\textasciitilde {n}}ate, Jos{\\'{e}} and Millan, William and Mendoza, Luis Alfonso and S{\\'{a}}nchez, Carlos Guillermo and Fernandez-Suarez, Hugo and Bonilla-Aldana, D. Katterine and Rodr{\\'{\\i}}guez-Morales, Alfonso J.\",\n",
      "    doi = \"10.1186/s12941-020-00358-y\",\n",
      "    year = \"2020\",\n",
      "    title = \"Successful recovery of COVID-19 pneumonia in a patient from Colombia after receiving chloroquine and clarithromycin\",\n",
      "    journal = \"Annals of Clinical Microbiology and Antimicrobials\"\n",
      "}\n",
      "@article{10.1186/s40779-020-0233-6,\n",
      "    author = \"Jin, Ying-Hui and and Lin Cai and Cheng, Zhen-Shun and Cheng, Hong and Deng, Tong and Fan, Yi-Pin and Fang, Cheng and Huang, Di and Huang, Lu-Qi and Huang, Qiao and Han, Yong and Hu, Bo and Hu, Fen and Li, Bing-Hui and Li, Yi-Rong and Liang, Ke and Lin, Li-Kai and Luo, Li-Sha and Ma, Jing and Ma, Lin-Lu and Peng, Zhi-Yong and Pan, Yun-Bao and Pan, Zhen-Yu and Ren, Xue-Qun and Sun, Hui-Min and Wang, Ying and Wang, Yun-Yun and Weng, Hong and Wei, Chao-Jie and Wu, Dong-Fang and Xia, Jian and Xiong, Yong and Xu, Hai-Bo and Yao, Xiao-Mei and Yuan, Yu-Feng and Ye, Tai-Sheng and Zhang, Xiao-Chun and Zhang, Ying-Wen and Zhang, Yin-Gao and Zhang, Hua-Min and Zhao, Yan and Zhao, Ming-Juan and Zi, Hao and Zeng, Xian-Tao and Wang, Yong-Yan and Wang, Xing-Huan\",\n",
      "    doi = \"10.1186/s40779-020-0233-6\",\n",
      "    year = \"2020\",\n",
      "    title = \"A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)\",\n",
      "    journal = \"Military Medical Research\"\n",
      "}\n",
      "@article{10.4274/balkanmedj.galenos.2020.2020.2.15,\n",
      "    author = \"An, Peng and Song, Ping and Lian, Kai and Wang, Yong\",\n",
      "    doi = \"10.4274/balkanmedj.galenos.2020.2020.2.15\",\n",
      "    year = \"2020\",\n",
      "    title = \"CT Manifestations of Novel Coronavirus Pneumonia: A Case Report\",\n",
      "    journal = \"Balkan Medical Journal\"\n",
      "}\n",
      "@article{10.7759/cureus.7352,\n",
      "    author = \"Filatov, Asia and Sharma, Pamraj and Hindi, Fawzi and Espinosa, Patricio S\",\n",
      "    doi = \"10.7759/cureus.7352\",\n",
      "    year = \"2020\",\n",
      "    title = \"Neurological Complications of Coronavirus Disease (COVID-19): Encephalopathy\",\n",
      "    journal = \"Cureus\"\n",
      "}\n",
      "@article{10.7759/cureus.7473,\n",
      "    author = \"Mukherjee, Aveek and Ahmad, Mudassar and Frenia, Douglas\",\n",
      "    doi = \"10.7759/cureus.7473\",\n",
      "    year = \"2020\",\n",
      "    title = \"A Coronavirus Disease 2019 (COVID-19) Patient with Multifocal Pneumonia Treated with Hydroxychloroquine\",\n",
      "    journal = \"Cureus\"\n",
      "}\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "@article{10.7759/cureus.7482,\n",
      "    author = \"Ahmed, Taha and Shah, Ronak J and Rahim, Shab E Gul and Flores, Monica and O{\\textquotesingle}Linn, Amy\",\n",
      "    doi = \"10.7759/cureus.7482\",\n",
      "    year = \"2020\",\n",
      "    title = \"Coronavirus Disease 2019 (COVID-19) Complicated by Acute Respiratory Distress Syndrome: An Internist's Perspective\",\n",
      "    journal = \"Cureus\"\n",
      "}\n",
      "@article{10.7759/cureus.7782,\n",
      "    author = \"Siddamreddy, Suman and Thotakura, Ramakrishna and Dandu, Vasuki and Kanuru, Sruthi and Meegada, Sreenath\",\n",
      "    doi = \"10.7759/cureus.7782\",\n",
      "    year = \"2020\",\n",
      "    title = \"Corona Virus Disease 2019 (COVID-19) Presenting as Acute ST Elevation Myocardial Infarction\",\n",
      "    journal = \"Cureus\"\n",
      "}\n"
     ]
    }
   ],
   "source": [
    "for doi in dmerge.csv.doi[~dmerge.csv.doi.isin(alreadyhave)].dropna().unique():\n",
    "    try:\n",
    "        res = doi2bib.crossref.get_bib(doi)\n",
    "        bib = bibtex.Parser().parse_string(res[1])\n",
    "        e = bib.entries[bib.entries.keys()[0]]\n",
    "        e.fields = dict(e.fields)\n",
    "        del e.fields[\"url\"]\n",
    "        del e.fields[\"month\"]\n",
    "        if \"volume\" in e.fields:\n",
    "            del e.fields[\"volume\"]\n",
    "        if \"number\" in e.fields:\n",
    "            del e.fields[\"number\"]\n",
    "        if \"pages\" in e.fields:\n",
    "            del e.fields[\"pages\"]\n",
    "        if \"publisher\" in e.fields:\n",
    "            del e.fields[\"publisher\"]\n",
    "        e.fields[\"title\"] = e.fields[\"title\"].replace(\"{\",\"\").replace(\"}\",\"\")\n",
    "        e.key = e.fields[\"doi\"].replace(\"(\",\"\").replace(\")\",\"\")\n",
    "        bib = bibtex.Parser()\n",
    "        bib.entries = dict({e.key:e})\n",
    "        bib.preamble = \"\"\n",
    "        a = pybtex.database.output.bibtex.Writer()\n",
    "        a.write_stream(bib, sys.stdout)\n",
    "    except:\n",
    "        pass"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 158,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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