PMID to DOI and PMCID using Biopython.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Dependencies\n",
    "import os\n",
    "import pandas as pd\n",
    "import numpy as np\n",
    "import requests\n",
    "import json\n",
    "from Bio import Entrez\n",
    "from Bio import Medline\n",
    "import pprint\n",
    "# import xml.etree.ElementTree as ET\n",
    "# from bs4 import BeautifulSoup as BS"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "cwd = os.getcwd()\n",
    "print(cwd)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "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>PMID</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1315666</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>1316830</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>1415137</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>1456336</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1519841</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      PMID\n",
       "0  1315666\n",
       "1  1316830\n",
       "2  1415137\n",
       "3  1456336\n",
       "4  1519841"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# upload PMID list\n",
    "# pmid_list = pd.read_csv(r\"C:\\Users\\keg827\\Documents\\10_Github_Repos\\pubmedbiopython\\cardiaids.csv\", encoding= 'unicode_escape')\n",
    "pmid_list = pd.read_csv(\"pmidcardia.csv\")\n",
    "pmid_list.head()\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "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>PMID</th>\n",
       "      <th>DOI</th>\n",
       "      <th>PMCID</th>\n",
       "      <th>DOI2</th>\n",
       "      <th>PMCID2</th>\n",
       "      <th>PMCID3</th>\n",
       "      <th>DOI3</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1315666</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>1316830</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>1415137</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>1456336</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1519841</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      PMID DOI PMCID DOI2 PMCID2 PMCID3 DOI3\n",
       "0  1315666                                  \n",
       "1  1316830                                  \n",
       "2  1415137                                  \n",
       "3  1456336                                  \n",
       "4  1519841                                  "
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# set up additional columns to hold information\n",
    "pmid_list['DOI'] = \"\"\n",
    "pmid_list['PMCID'] = \"\"\n",
    "pmid_list['DOI2'] = \"\"\n",
    "pmid_list['PMCID2'] = \"\"\n",
    "pmid_list['PMCID3'] = \"\"\n",
    "pmid_list['DOI3'] = \"\"\n",
    "pmid_list.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Retrieving DOI from PMID1315666.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID1316830.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID1415137.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID1456336.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID1519841.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID1526025.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID1536331.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID1549006.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID1570801.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID1580246.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID1739373.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID1851696.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID1884448.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID1918764.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID1951168.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID1969463.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID1983903.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID1989788.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID2011649.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID2031493.\n",
      "The DOI is: 10.1093/ajcn/53.6.1604S\n",
      "------------\n",
      "Retrieving DOI from PMID2037862.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID2063831.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID2084017.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID2188641.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID2193307.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID2200851.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID2204367.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID2204915.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID2273523.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID2382740.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID2683750.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID2759681.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID2783079.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID3204420.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID3261566.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID3440391.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID7485047.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID7485815.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID7502103.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID7580711.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID7634452.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID7641357.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID7722583.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID7742729.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID7797754.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID7830019.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID7872189.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID7884094.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID7897300.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID7921312.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID7965210.\n",
      "The DOI is: 10.1093/jn/124.suppl_11.2245s\n",
      "------------\n",
      "Retrieving DOI from PMID7980844.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID7981840.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8003274.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8021418.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8081431.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8172846.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8196117.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8213754.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8229103.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8266905.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8318505.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8371651.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8389336.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8404773.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8416117.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8466495.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8520711.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8598425.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8604777.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8610688.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8611277.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8611278.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8616942.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8633619.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8686692.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8686693.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8727231.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8759809.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8775596.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8788322.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8827159.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8827799.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8876504.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8879349.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8946271.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID9003130.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID9006307.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID9012637.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID9017509.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID9024231.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID9031018.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID9146443.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID9146444.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID9245672.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID9286933.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID9308507.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID9321742.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID9326433.\n",
      "Missing field/result... skipping.\n",
      "------------\n"
     ]
    },
    {
     "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>PMID</th>\n",
       "      <th>DOI</th>\n",
       "      <th>PMCID</th>\n",
       "      <th>DOI2</th>\n",
       "      <th>PMCID2</th>\n",
       "      <th>PMCID3</th>\n",
       "      <th>DOI3</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1315666</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>1316830</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>1415137</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>1456336</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1519841</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>94</th>\n",
       "      <td>9245672</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>95</th>\n",
       "      <td>9286933</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>96</th>\n",
       "      <td>9308507</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>97</th>\n",
       "      <td>9321742</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>98</th>\n",
       "      <td>9326433</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>99 rows × 7 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       PMID DOI PMCID DOI2 PMCID2 PMCID3 DOI3\n",
       "0   1315666                                  \n",
       "1   1316830                                  \n",
       "2   1415137                                  \n",
       "3   1456336                                  \n",
       "4   1519841                                  \n",
       "..      ...  ..   ...  ...    ...    ...  ...\n",
       "94  9245672                                  \n",
       "95  9286933                                  \n",
       "96  9308507                                  \n",
       "97  9321742                                  \n",
       "98  9326433                                  \n",
       "\n",
       "[99 rows x 7 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "##################################################\n",
    "## Get DOI from PMID using Biopython ENTREZ READ\n",
    "##################################################\n",
    "\n",
    "# Use iterrows to iterate through pandas pmid_list dataframe\n",
    "for index, row in pmid_list.iterrows():\n",
    "\n",
    "    PMID = row[\"PMID\"]\n",
    "    api_key = \"9f4f75f5531d495aa2df93ea54696b607b08\"\n",
    "    Entrez.email = \"karen.gutzman@northwestern.edu\"\n",
    "    handle = Entrez.efetch(db=\"pubmed\", id=PMID, api_key=api_key, retmode=\"xml\")\n",
    "    #records = Entrez.parse(handle)\n",
    "    \n",
    "    #THe Entrez.read() function parses an XML file created by NCBI's Entrez Utilities, returning a multilevel data structure of Python \n",
    "    #lists and dictionaries. Most XML files returned by NCBI's Entrez Utilities can be parsed by this function, provided \n",
    "    #its DTD is available. Biopython includes the DTDs for most commonly used Entrez Utilities.\n",
    "    records = Entrez.read(handle)\n",
    "    \n",
    "    try:\n",
    "        print(f\"Retrieving DOI from PMID{PMID}.\") \n",
    "        #for item in records:\n",
    "            # each record is a Python dictionary or list.\n",
    "        DOI = records[\"PubmedArticle\"][0][\"MedlineCitation\"][\"Article\"][\"ELocationID\"][0]\n",
    "        print(f\"The DOI is: {DOI}\")\n",
    "           \n",
    "        ##Extra Testing Code\n",
    "        \n",
    "        #records = Entrez.parse(handle)\n",
    "        #print(record[3])\n",
    "        #print(records)\n",
    "        #pp = pprint.PrettyPrinter(indent=1)\n",
    "        #pp.pprint(records)\n",
    "        \n",
    "        ## Add DOI to the PMID_List file in a new column called DOI\n",
    "        pmid_list.loc[index, 'DOI'] = DOI\n",
    "        #types_df.loc[index, 'address'] = results[0]['vicinity']\n",
    "               \n",
    "    \n",
    "    except (KeyError, IndexError):\n",
    "        print(\"Missing field/result... skipping.\")\n",
    "        \n",
    "    print(\"------------\")\n",
    "    \n",
    "    \n",
    "handle.close()    \n",
    "pmid_list\n",
    "    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Retrieving PMCID from PMID1315666.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID1316830.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID1415137.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID1456336.\n",
      "1694535\n",
      "------------\n",
      "Retrieving PMCID from PMID1519841.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID1526025.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID1536331.\n",
      "1694439\n",
      "------------\n",
      "Retrieving PMCID from PMID1549006.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID1570801.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID1580246.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID1739373.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID1851696.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID1884448.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID1918764.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID1951168.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID1969463.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID1983903.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID1989788.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID2011649.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID2031493.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID2037862.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID2063831.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID2084017.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID2188641.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID2193307.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID2200851.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID2204367.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID2204915.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID2273523.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID2382740.\n",
      "1404871\n",
      "------------\n",
      "Retrieving PMCID from PMID2683750.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID2759681.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID2783079.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID3204420.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID3261566.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID3440391.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID7485047.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID7485815.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID7502103.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID7580711.\n",
      "2551059\n",
      "------------\n",
      "Retrieving PMCID from PMID7634452.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID7641357.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID7722583.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID7742729.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID7797754.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID7830019.\n",
      "1060043\n",
      "------------\n",
      "Retrieving PMCID from PMID7872189.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID7884094.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID7897300.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID7921312.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID7965210.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID7980844.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID7981840.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8003274.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8021418.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8081431.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8172846.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8196117.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8213754.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8229103.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8266905.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8318505.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8371651.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8389336.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8404773.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8416117.\n",
      "1403434\n",
      "------------\n",
      "Retrieving PMCID from PMID8466495.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8520711.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8598425.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8604777.\n",
      "1380547\n",
      "------------\n",
      "Retrieving PMCID from PMID8610688.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8611277.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8611278.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8616942.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8633619.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8686692.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8686693.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8727231.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8759809.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8775596.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8788322.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8827159.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8827799.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8876504.\n",
      "1380646\n",
      "------------\n",
      "Retrieving PMCID from PMID8879349.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID8946271.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID9003130.\n",
      "1380726\n",
      "------------\n",
      "Retrieving PMCID from PMID9006307.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID9012637.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID9017509.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID9024231.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID9031018.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID9146443.\n",
      "1380844\n",
      "------------\n",
      "Retrieving PMCID from PMID9146444.\n",
      "1380845\n",
      "------------\n",
      "Retrieving PMCID from PMID9245672.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID9286933.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID9308507.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID9321742.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving PMCID from PMID9326433.\n",
      "Missing field/result... skipping.\n",
      "------------\n"
     ]
    },
    {
     "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>PMID</th>\n",
       "      <th>DOI</th>\n",
       "      <th>PMCID</th>\n",
       "      <th>DOI2</th>\n",
       "      <th>PMCID2</th>\n",
       "      <th>PMCID3</th>\n",
       "      <th>DOI3</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1315666</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>1316830</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>1415137</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>1456336</td>\n",
       "      <td></td>\n",
       "      <td>1694535</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1519841</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>94</th>\n",
       "      <td>9245672</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>95</th>\n",
       "      <td>9286933</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>96</th>\n",
       "      <td>9308507</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>97</th>\n",
       "      <td>9321742</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>98</th>\n",
       "      <td>9326433</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>99 rows × 7 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       PMID DOI    PMCID DOI2 PMCID2 PMCID3 DOI3\n",
       "0   1315666                                     \n",
       "1   1316830                                     \n",
       "2   1415137                                     \n",
       "3   1456336      1694535                        \n",
       "4   1519841                                     \n",
       "..      ...  ..      ...  ...    ...    ...  ...\n",
       "94  9245672                                     \n",
       "95  9286933                                     \n",
       "96  9308507                                     \n",
       "97  9321742                                     \n",
       "98  9326433                                     \n",
       "\n",
       "[99 rows x 7 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#####################################################\n",
    "## Get PMCID from PMID using Biopython ENTREZ ELINK\n",
    "#####################################################\n",
    "\n",
    "# Use iterrows to iterate through pandas pmid_list dataframe\n",
    "for index, row in pmid_list.iterrows():\n",
    "\n",
    "    PMID = row[\"PMID\"]\n",
    "    api_key = \"9f4f75f5531d495aa2df93ea54696b607b08\"\n",
    "    Entrez.email = \"karen.gutzman@northwestern.edu\"\n",
    "    handle = Entrez.elink(dbfrom=\"pubmed\", db=\"pmc\", linkname=\"pubmed_pmc\", id=PMID, retmode=\"text\", retmax = \"400\")\n",
    "    records = Entrez.read(handle)\n",
    "    try:\n",
    "        print(f\"Retrieving PMCID from PMID{PMID}.\") \n",
    "        for item in records: \n",
    "       # each record is a Python dictionary or list.\n",
    "            PMCID = item['LinkSetDb'][0]['Link'][0]['Id']\n",
    "            print(PMCID)\n",
    "         ## Add PMCID to the PMID_List file in a new column called PMCID\n",
    "        pmid_list.loc[index, 'PMCID'] = PMCID\n",
    "\n",
    "    except (KeyError, IndexError):\n",
    "        print(\"Missing field/result... skipping.\")\n",
    "        \n",
    "    print(\"------------\")\n",
    "    \n",
    "    \n",
    "handle.close()    \n",
    "pmid_list"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Retrieving DOI from PMID1315666.\n",
      "0197-2456(92)90031-T\n",
      "This is DOI2 0197-2456(92)90031-T\n",
      "This is DOI3 10.1016/0197-2456(92)90031-t\n",
      "------------\n",
      "Retrieving DOI from PMID1316830.\n",
      "0197-2456(92)90021-Q\n",
      "This is DOI2 0197-2456(92)90021-Q\n",
      "This is DOI3 10.1016/0197-2456(92)90021-q\n",
      "------------\n",
      "Retrieving DOI from PMID1415137.\n",
      "10.1093/oxfordjournals.aje.a116480\n",
      "This is DOI2 10.1093/oxfordjournals.aje.a116480\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID1456336.\n",
      "PMC1694535\n",
      "This is PMID2 PMC1694535\n",
      "This is DOI3 10.2105/ajph.82.12.1621\n",
      "------------\n",
      "Retrieving DOI from PMID1519841.\n",
      "10.1164/ajrccm/146.3.644\n",
      "This is DOI2 10.1164/ajrccm/146.3.644\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID1526025.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID1536331.\n",
      "PMC1694439\n",
      "This is PMID2 PMC1694439\n",
      "This is DOI3 10.2105/ajph.82.1.33\n",
      "------------\n",
      "Retrieving DOI from PMID1549006.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID1570801.\n",
      "10.1093/ajcn/55.5.943\n",
      "This is DOI2 10.1093/ajcn/55.5.943\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID1580246.\n",
      "10.1093/oxfordjournals.aje.a116349\n",
      "This is DOI2 10.1093/oxfordjournals.aje.a116349\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID1739373.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID1851696.\n",
      "10.1016/0197-2456(91)90002-4\n",
      "This is DOI2 10.1016/0197-2456(91)90002-4\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID1884448.\n",
      "10.1161/01.cir.84.3.1176\n",
      "This is DOI2 10.1161/01.cir.84.3.1176\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID1918764.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID1951168.\n",
      "10.1093/ajcn/54.5.930\n",
      "This is DOI2 10.1093/ajcn/54.5.930\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID1969463.\n",
      "0895-4356(90)90050-Y\n",
      "This is DOI2 0895-4356(90)90050-Y\n",
      "This is DOI3 10.1016/0895-4356(90)90050-y\n",
      "------------\n",
      "Retrieving DOI from PMID1983903.\n",
      "10.1093/oxfordjournals.aje.a115807\n",
      "This is DOI2 10.1093/oxfordjournals.aje.a115807\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID1989788.\n",
      "S0012-3692(16)48830-6\n",
      "This is DOI2 S0012-3692(16)48830-6\n",
      "This is DOI3 10.1378/chest.99.2.315\n",
      "------------\n",
      "Retrieving DOI from PMID2011649.\n",
      "10.1097/00006842-199101000-00004\n",
      "This is DOI2 10.1097/00006842-199101000-00004\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID2031493.\n",
      "10.1093/ajcn/53.6.1604S\n",
      "This is DOI2 10.1093/ajcn/53.6.1604S\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID2037862.\n",
      "0895-4356(91)90221-T\n",
      "This is DOI2 0895-4356(91)90221-T\n",
      "This is DOI3 10.1016/0895-4356(91)90221-t\n",
      "------------\n",
      "Retrieving DOI from PMID2063831.\n",
      "10.1093/oxfordjournals.aje.a115835\n",
      "This is DOI2 10.1093/oxfordjournals.aje.a115835\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID2084017.\n",
      "10.1093/ije/19.4.889\n",
      "This is DOI2 10.1093/ije/19.4.889\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID2188641.\n",
      "10.1161/01.atv.10.3.430\n",
      "This is DOI2 10.1161/01.atv.10.3.430\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID2193307.\n",
      "10.1016/0091-7435(90)90017-e\n",
      "This is DOI2 10.1016/0091-7435(90)90017-e\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID2200851.\n",
      "0895-4356(90)90240-P\n",
      "This is DOI2 0895-4356(90)90240-P\n",
      "This is DOI3 10.1016/0895-4356(90)90240-p\n",
      "------------\n",
      "Retrieving DOI from PMID2204367.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID2204915.\n",
      "10.1016/0091-7435(90)90045-l\n",
      "This is DOI2 10.1016/0091-7435(90)90045-l\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID2273523.\n",
      "10.1007/BF00844831\n",
      "This is DOI2 10.1007/BF00844831\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID2382740.\n",
      "PMC1404871\n",
      "This is PMID2 PMC1404871\n",
      "This is DOI3 10.2105/ajph.80.9.1053\n",
      "------------\n",
      "Retrieving DOI from PMID2683750.\n",
      "10.1093/oxfordjournals.aje.a115424\n",
      "This is DOI2 10.1093/oxfordjournals.aje.a115424\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID2759681.\n",
      "10.1161/01.hyp.14.2.218\n",
      "This is DOI2 10.1161/01.hyp.14.2.218\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID2783079.\n",
      "10.1161/01.atv.9.5.656\n",
      "This is DOI2 10.1161/01.atv.9.5.656\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID3204420.\n",
      "0895-4356(88)90080-7\n",
      "This is DOI2 0895-4356(88)90080-7\n",
      "This is DOI3 10.1016/0895-4356(88)90080-7\n",
      "------------\n",
      "Retrieving DOI from PMID3261566.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID3440391.\n",
      "0197-2456(87)90008-0\n",
      "This is DOI2 0197-2456(87)90008-0\n",
      "This is DOI3 10.1016/0197-2456(87)90008-0\n",
      "------------\n",
      "Retrieving DOI from PMID7485047.\n",
      "10.1093/oxfordjournals.aje.a117555\n",
      "This is DOI2 10.1093/oxfordjournals.aje.a117555\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID7485815.\n",
      "10.1111/j.1530-0277.1995.tb00987.x\n",
      "This is DOI2 10.1111/j.1530-0277.1995.tb00987.x\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID7502103.\n",
      "0277953694003857\n",
      "This is DOI2 0277953694003857\n",
      "This is DOI3 10.1016/0277-9536(94)00385-7\n",
      "------------\n",
      "Retrieving DOI from PMID7580711.\n",
      "PMC2551059\n",
      "This is PMID2 PMC2551059\n",
      "This is DOI3 10.1136/bmj.311.7013.1139\n",
      "------------\n",
      "Retrieving DOI from PMID7634452.\n",
      "10.1161/01.cir.92.3.380\n",
      "This is DOI2 10.1161/01.cir.92.3.380\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID7641357.\n",
      "10.1161/01.cir.92.4.785\n",
      "This is DOI2 10.1161/01.cir.92.4.785\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID7722583.\n",
      "0895-4356(94)90166-X\n",
      "This is DOI2 0895-4356(94)90166-X\n",
      "This is DOI3 10.1016/0895-4356(94)90166-x\n",
      "------------\n",
      "Retrieving DOI from PMID7742729.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID7797754.\n",
      "073510979500118J\n",
      "This is DOI2 073510979500118J\n",
      "This is DOI3 10.1016/0735-1097(95)00118-j\n",
      "------------\n",
      "Retrieving DOI from PMID7830019.\n",
      "PMC1060043\n",
      "This is PMID2 PMC1060043\n",
      "This is DOI3 10.1136/jech.48.6.604\n",
      "------------\n",
      "Retrieving DOI from PMID7872189.\n",
      "0002-8703(95)90287-2\n",
      "This is DOI2 0002-8703(95)90287-2\n",
      "This is DOI3 10.1016/0002-8703(95)90287-2\n",
      "------------\n",
      "Retrieving DOI from PMID7884094.\n",
      "0735-1097(94)00469-7\n",
      "This is DOI2 0735-1097(94)00469-7\n",
      "This is DOI3 10.1016/0735-1097(94)00469-7\n",
      "------------\n",
      "Retrieving DOI from PMID7897300.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID7921312.\n",
      "1047-2797(93)90087-K\n",
      "This is DOI2 1047-2797(93)90087-K\n",
      "This is DOI3 10.1016/1047-2797(93)90087-k\n",
      "------------\n",
      "Retrieving DOI from PMID7965210.\n",
      "10.1093/jn/124.suppl_11.2245s\n",
      "This is DOI2 10.1093/jn/124.suppl_11.2245s\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID7980844.\n",
      "10.1093/oxfordjournals.aje.a117311\n",
      "This is DOI2 10.1093/oxfordjournals.aje.a117311\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID7981840.\n",
      "1047-2797(94)90067-1\n",
      "This is DOI2 1047-2797(94)90067-1\n",
      "This is DOI3 10.1016/1047-2797(94)90067-1\n",
      "------------\n",
      "Retrieving DOI from PMID8003274.\n",
      "0895-7061(94)90104-X\n",
      "This is DOI2 0895-7061(94)90104-X\n",
      "This is DOI3 10.1093/ajh/7.3.234\n",
      "------------\n",
      "Retrieving DOI from PMID8021418.\n",
      "0002-8223(94)91944-5\n",
      "This is DOI2 0002-8223(94)91944-5\n",
      "This is DOI3 10.1016/0002-8223(94)91944-5\n",
      "------------\n",
      "Retrieving DOI from PMID8081431.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8172846.\n",
      "10.1161/01.atv.14.5.686\n",
      "This is DOI2 10.1161/01.atv.14.5.686\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8196117.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8213754.\n",
      "10.1093/oxfordjournals.aje.a116884\n",
      "This is DOI2 10.1093/oxfordjournals.aje.a116884\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8229103.\n",
      "0895-4356(93)90090-N\n",
      "This is DOI2 0895-4356(93)90090-N\n",
      "This is DOI3 10.1016/0895-4356(93)90090-n\n",
      "------------\n",
      "Retrieving DOI from PMID8266905.\n",
      "10.1093/oxfordjournals.aje.a116821\n",
      "This is DOI2 10.1093/oxfordjournals.aje.a116821\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8318505.\n",
      "10.1161/01.atv.13.7.1037\n",
      "This is DOI2 10.1161/01.atv.13.7.1037\n",
      "Missing field/result... skipping.\n",
      "------------\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Retrieving DOI from PMID8371651.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8389336.\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8404773.\n",
      "S0013-9351(83)71124-2\n",
      "This is DOI2 S0013-9351(83)71124-2\n",
      "This is DOI3 10.1006/enrs.1993.1124\n",
      "------------\n",
      "Retrieving DOI from PMID8416117.\n",
      "PMC1403434\n",
      "This is PMID2 PMC1403434\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8466495.\n",
      "S0006-291X(83)71343-4\n",
      "This is DOI2 S0006-291X(83)71343-4\n",
      "This is DOI3 10.1006/bbrc.1993.1343\n",
      "------------\n",
      "Retrieving DOI from PMID8520711.\n",
      "1047-2797(94)00095-B\n",
      "This is DOI2 1047-2797(94)00095-B\n",
      "This is DOI3 10.1016/1047-2797(94)00095-b\n",
      "------------\n",
      "Retrieving DOI from PMID8598425.\n",
      "10.1080/07315724.1995.10718553\n",
      "This is DOI2 10.1080/07315724.1995.10718553\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8604777.\n",
      "PMC1380547\n",
      "This is PMID2 PMC1380547\n",
      "This is DOI3 10.2105/ajph.86.4.480\n",
      "------------\n",
      "Retrieving DOI from PMID8610688.\n",
      "10.1093/oxfordjournals.aje.a008816\n",
      "This is DOI2 10.1093/oxfordjournals.aje.a008816\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8611277.\n",
      "S0894-7317(05)80001-X\n",
      "This is DOI2 S0894-7317(05)80001-X\n",
      "This is DOI3 10.1016/s0894-7317(05)80001-x\n",
      "------------\n",
      "Retrieving DOI from PMID8611278.\n",
      "S0894-7317(05)80002-1\n",
      "This is DOI2 S0894-7317(05)80002-1\n",
      "This is DOI3 10.1016/s0894-7317(05)80002-1\n",
      "------------\n",
      "Retrieving DOI from PMID8616942.\n",
      "10.1161/01.cir.93.1.60\n",
      "This is DOI2 10.1161/01.cir.93.1.60\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8633619.\n",
      "10.1093/oxfordjournals.aje.a008749\n",
      "This is DOI2 10.1093/oxfordjournals.aje.a008749\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8686692.\n",
      "10.1093/oxfordjournals.aje.a008918\n",
      "This is DOI2 10.1093/oxfordjournals.aje.a008918\n",
      "Missing field/result... skipping.\n",
      "------------\n",
      "Retrieving DOI from PMID8686693.\n",
      "10.1093/oxfordjournals.aje.a008919\n",
      "This is DOI2 10.1093/oxfordjournals.aje.a008919\n",
      "Missing field/result... skipping.\n",
      "------------\n"
     ]
    }
   ],
   "source": [
    "#####################################################\n",
    "## Get PMCID from PMID using Biopython ENTREZ READ\n",
    "#####################################################\n",
    "\n",
    "# Use iterrows to iterate through pandas pmid_list dataframe\n",
    "for index, row in pmid_list.iterrows():\n",
    "\n",
    "    PMID = row[\"PMID\"]\n",
    "    api_key = \"9f4f75f5531d495aa2df93ea54696b607b08\"\n",
    "    Entrez.email = \"karen.gutzman@northwestern.edu\"\n",
    "    handle = Entrez.efetch(db=\"pubmed\", id=PMID, api_key=api_key, retmode=\"xml\")\n",
    "    records = Entrez.read(handle)\n",
    "#     ID_dict = {}\n",
    "    PMCID2= 'none'\n",
    "    PMCID3 = 'none'\n",
    "    DOI2=\"none\"\n",
    "    DOI3 = \"none\"\n",
    "    try:\n",
    "        print(f\"Retrieving DOI from PMID{PMID}.\") \n",
    "        #for item in records:\n",
    "            # each record is a Python dictionary or list.\n",
    "        ArtID2 = records[\"PubmedArticle\"][0]['PubmedData']['ArticleIdList'][1]\n",
    "        print(ArtID2)\n",
    "        PMCSTART = \"P\"\n",
    "#         using list comprehension + startswith() + lower() \n",
    "#         Words starting with specific letter \n",
    "       \n",
    "        if ArtID2.lower().startswith(PMCSTART.lower()):\n",
    "            PMCID2 = ArtID2\n",
    "            print(f\"This is PMID2 {PMCID2}\")\n",
    "        else:\n",
    "            DOI2 =ArtID2\n",
    "            print(f\"This is DOI2 {DOI2}\")\n",
    "        \n",
    "        \n",
    "        ## Add DOI to the PMID_List file in a new column called DOI\n",
    "        pmid_list.loc[index, 'DOI2'] = DOI2\n",
    "        pmid_list.loc[index, 'PMCID2'] = PMCID2\n",
    "        \n",
    "        ArtID3 = records[\"PubmedArticle\"][0]['PubmedData']['ArticleIdList'][2]\n",
    "        \n",
    "        if ArtID3.lower().startswith(PMCSTART.lower()):\n",
    "            PMCID3 = ArtID3\n",
    "            print(f\"This is PMID3 {PMCID3}\")\n",
    "        else:\n",
    "            DOI3 =ArtID3\n",
    "            print(f\"This is DOI3 {DOI3}\")\n",
    "        \n",
    "        \n",
    "        ## Add DOI to the PMID_List file in a new column called DOI\n",
    "        pmid_list.loc[index, 'DOI3'] = DOI3\n",
    "        pmid_list.loc[index, 'PMCID3'] = PMCID3\n",
    "                       \n",
    "    \n",
    "    except (KeyError, IndexError):\n",
    "        print(\"Missing field/result... skipping.\")\n",
    "        \n",
    "    print(\"------------\")\n",
    "    \n",
    "    \n",
    "handle.close()    \n",
    "pmid_list"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Save Data to csv\n",
    "pmid_list.to_csv(\"PMIDtoDOIPMCID.csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Retrieving DOI from PMID1315666.\n",
      "[StringElement('1315666', attributes={'IdType': 'pubmed'}), StringElement('0197-2456(92)90031-T', attributes={'IdType': 'pii'}), StringElement('10.1016/0197-2456(92)90031-t', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID1316830.\n",
      "[StringElement('1316830', attributes={'IdType': 'pubmed'}), StringElement('0197-2456(92)90021-Q', attributes={'IdType': 'pii'}), StringElement('10.1016/0197-2456(92)90021-q', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID1415137.\n",
      "[StringElement('1415137', attributes={'IdType': 'pubmed'}), StringElement('10.1093/oxfordjournals.aje.a116480', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID1456336.\n",
      "[StringElement('1456336', attributes={'IdType': 'pubmed'}), StringElement('PMC1694535', attributes={'IdType': 'pmc'}), StringElement('10.2105/ajph.82.12.1621', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID1519841.\n",
      "[StringElement('1519841', attributes={'IdType': 'pubmed'}), StringElement('10.1164/ajrccm/146.3.644', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID1526025.\n",
      "[StringElement('1526025', attributes={'IdType': 'pubmed'})]\n",
      "------------\n",
      "Retrieving DOI from PMID1536331.\n",
      "[StringElement('1536331', attributes={'IdType': 'pubmed'}), StringElement('PMC1694439', attributes={'IdType': 'pmc'}), StringElement('10.2105/ajph.82.1.33', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID1549006.\n",
      "[StringElement('1549006', attributes={'IdType': 'pubmed'})]\n",
      "------------\n",
      "Retrieving DOI from PMID1570801.\n",
      "[StringElement('1570801', attributes={'IdType': 'pubmed'}), StringElement('10.1093/ajcn/55.5.943', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID1580246.\n",
      "[StringElement('1580246', attributes={'IdType': 'pubmed'}), StringElement('10.1093/oxfordjournals.aje.a116349', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID1739373.\n",
      "[StringElement('1739373', attributes={'IdType': 'pubmed'})]\n",
      "------------\n",
      "Retrieving DOI from PMID1851696.\n",
      "[StringElement('1851696', attributes={'IdType': 'pubmed'}), StringElement('10.1016/0197-2456(91)90002-4', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID1884448.\n",
      "[StringElement('1884448', attributes={'IdType': 'pubmed'}), StringElement('10.1161/01.cir.84.3.1176', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID1918764.\n",
      "[StringElement('1918764', attributes={'IdType': 'pubmed'})]\n",
      "------------\n",
      "Retrieving DOI from PMID1951168.\n",
      "[StringElement('1951168', attributes={'IdType': 'pubmed'}), StringElement('10.1093/ajcn/54.5.930', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID1969463.\n",
      "[StringElement('1969463', attributes={'IdType': 'pubmed'}), StringElement('0895-4356(90)90050-Y', attributes={'IdType': 'pii'}), StringElement('10.1016/0895-4356(90)90050-y', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID1983903.\n",
      "[StringElement('1983903', attributes={'IdType': 'pubmed'}), StringElement('10.1093/oxfordjournals.aje.a115807', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID1989788.\n",
      "[StringElement('1989788', attributes={'IdType': 'pubmed'}), StringElement('S0012-3692(16)48830-6', attributes={'IdType': 'pii'}), StringElement('10.1378/chest.99.2.315', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID2011649.\n",
      "[StringElement('2011649', attributes={'IdType': 'pubmed'}), StringElement('10.1097/00006842-199101000-00004', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID2031493.\n",
      "[StringElement('2031493', attributes={'IdType': 'pubmed'}), StringElement('10.1093/ajcn/53.6.1604S', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID2037862.\n",
      "[StringElement('2037862', attributes={'IdType': 'pubmed'}), StringElement('0895-4356(91)90221-T', attributes={'IdType': 'pii'}), StringElement('10.1016/0895-4356(91)90221-t', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID2063831.\n",
      "[StringElement('2063831', attributes={'IdType': 'pubmed'}), StringElement('10.1093/oxfordjournals.aje.a115835', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID2084017.\n",
      "[StringElement('2084017', attributes={'IdType': 'pubmed'}), StringElement('10.1093/ije/19.4.889', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID2188641.\n",
      "[StringElement('2188641', attributes={'IdType': 'pubmed'}), StringElement('10.1161/01.atv.10.3.430', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID2193307.\n",
      "[StringElement('2193307', attributes={'IdType': 'pubmed'}), StringElement('10.1016/0091-7435(90)90017-e', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID2200851.\n",
      "[StringElement('2200851', attributes={'IdType': 'pubmed'}), StringElement('0895-4356(90)90240-P', attributes={'IdType': 'pii'}), StringElement('10.1016/0895-4356(90)90240-p', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID2204367.\n",
      "[StringElement('2204367', attributes={'IdType': 'pubmed'})]\n",
      "------------\n",
      "Retrieving DOI from PMID2204915.\n",
      "[StringElement('2204915', attributes={'IdType': 'pubmed'}), StringElement('10.1016/0091-7435(90)90045-l', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID2273523.\n",
      "[StringElement('2273523', attributes={'IdType': 'pubmed'}), StringElement('10.1007/BF00844831', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID2382740.\n",
      "[StringElement('2382740', attributes={'IdType': 'pubmed'}), StringElement('PMC1404871', attributes={'IdType': 'pmc'}), StringElement('10.2105/ajph.80.9.1053', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID2683750.\n",
      "[StringElement('2683750', attributes={'IdType': 'pubmed'}), StringElement('10.1093/oxfordjournals.aje.a115424', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID2759681.\n",
      "[StringElement('2759681', attributes={'IdType': 'pubmed'}), StringElement('10.1161/01.hyp.14.2.218', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID2783079.\n",
      "[StringElement('2783079', attributes={'IdType': 'pubmed'}), StringElement('10.1161/01.atv.9.5.656', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID3204420.\n",
      "[StringElement('3204420', attributes={'IdType': 'pubmed'}), StringElement('0895-4356(88)90080-7', attributes={'IdType': 'pii'}), StringElement('10.1016/0895-4356(88)90080-7', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID3261566.\n",
      "[StringElement('3261566', attributes={'IdType': 'pubmed'})]\n",
      "------------\n",
      "Retrieving DOI from PMID3440391.\n",
      "[StringElement('3440391', attributes={'IdType': 'pubmed'}), StringElement('0197-2456(87)90008-0', attributes={'IdType': 'pii'}), StringElement('10.1016/0197-2456(87)90008-0', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID7485047.\n",
      "[StringElement('7485047', attributes={'IdType': 'pubmed'}), StringElement('10.1093/oxfordjournals.aje.a117555', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID7485815.\n",
      "[StringElement('7485815', attributes={'IdType': 'pubmed'}), StringElement('10.1111/j.1530-0277.1995.tb00987.x', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID7502103.\n",
      "[StringElement('7502103', attributes={'IdType': 'pubmed'}), StringElement('0277953694003857', attributes={'IdType': 'pii'}), StringElement('10.1016/0277-9536(94)00385-7', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID7580711.\n",
      "[StringElement('7580711', attributes={'IdType': 'pubmed'}), StringElement('PMC2551059', attributes={'IdType': 'pmc'}), StringElement('10.1136/bmj.311.7013.1139', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID7634452.\n",
      "[StringElement('7634452', attributes={'IdType': 'pubmed'}), StringElement('10.1161/01.cir.92.3.380', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID7641357.\n",
      "[StringElement('7641357', attributes={'IdType': 'pubmed'}), StringElement('10.1161/01.cir.92.4.785', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID7722583.\n",
      "[StringElement('7722583', attributes={'IdType': 'pubmed'}), StringElement('0895-4356(94)90166-X', attributes={'IdType': 'pii'}), StringElement('10.1016/0895-4356(94)90166-x', attributes={'IdType': 'doi'})]\n",
      "------------\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Retrieving DOI from PMID7742729.\n",
      "[StringElement('7742729', attributes={'IdType': 'pubmed'})]\n",
      "------------\n",
      "Retrieving DOI from PMID7797754.\n",
      "[StringElement('7797754', attributes={'IdType': 'pubmed'}), StringElement('073510979500118J', attributes={'IdType': 'pii'}), StringElement('10.1016/0735-1097(95)00118-j', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID7830019.\n",
      "[StringElement('7830019', attributes={'IdType': 'pubmed'}), StringElement('PMC1060043', attributes={'IdType': 'pmc'}), StringElement('10.1136/jech.48.6.604', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID7872189.\n",
      "[StringElement('7872189', attributes={'IdType': 'pubmed'}), StringElement('0002-8703(95)90287-2', attributes={'IdType': 'pii'}), StringElement('10.1016/0002-8703(95)90287-2', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID7884094.\n",
      "[StringElement('7884094', attributes={'IdType': 'pubmed'}), StringElement('0735-1097(94)00469-7', attributes={'IdType': 'pii'}), StringElement('10.1016/0735-1097(94)00469-7', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID7897300.\n",
      "[StringElement('7897300', attributes={'IdType': 'pubmed'})]\n",
      "------------\n",
      "Retrieving DOI from PMID7921312.\n",
      "[StringElement('7921312', attributes={'IdType': 'pubmed'}), StringElement('1047-2797(93)90087-K', attributes={'IdType': 'pii'}), StringElement('10.1016/1047-2797(93)90087-k', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID7965210.\n",
      "[StringElement('7965210', attributes={'IdType': 'pubmed'}), StringElement('10.1093/jn/124.suppl_11.2245s', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID7980844.\n",
      "[StringElement('7980844', attributes={'IdType': 'pubmed'}), StringElement('10.1093/oxfordjournals.aje.a117311', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID7981840.\n",
      "[StringElement('7981840', attributes={'IdType': 'pubmed'}), StringElement('1047-2797(94)90067-1', attributes={'IdType': 'pii'}), StringElement('10.1016/1047-2797(94)90067-1', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8003274.\n",
      "[StringElement('8003274', attributes={'IdType': 'pubmed'}), StringElement('0895-7061(94)90104-X', attributes={'IdType': 'pii'}), StringElement('10.1093/ajh/7.3.234', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8021418.\n",
      "[StringElement('8021418', attributes={'IdType': 'pubmed'}), StringElement('0002-8223(94)91944-5', attributes={'IdType': 'pii'}), StringElement('10.1016/0002-8223(94)91944-5', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8081431.\n",
      "[StringElement('8081431', attributes={'IdType': 'pubmed'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8172846.\n",
      "[StringElement('8172846', attributes={'IdType': 'pubmed'}), StringElement('10.1161/01.atv.14.5.686', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8196117.\n",
      "[StringElement('8196117', attributes={'IdType': 'pubmed'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8213754.\n",
      "[StringElement('8213754', attributes={'IdType': 'pubmed'}), StringElement('10.1093/oxfordjournals.aje.a116884', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8229103.\n",
      "[StringElement('8229103', attributes={'IdType': 'pubmed'}), StringElement('0895-4356(93)90090-N', attributes={'IdType': 'pii'}), StringElement('10.1016/0895-4356(93)90090-n', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8266905.\n",
      "[StringElement('8266905', attributes={'IdType': 'pubmed'}), StringElement('10.1093/oxfordjournals.aje.a116821', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8318505.\n",
      "[StringElement('8318505', attributes={'IdType': 'pubmed'}), StringElement('10.1161/01.atv.13.7.1037', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8371651.\n",
      "[StringElement('8371651', attributes={'IdType': 'pubmed'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8389336.\n",
      "[StringElement('8389336', attributes={'IdType': 'pubmed'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8404773.\n",
      "[StringElement('8404773', attributes={'IdType': 'pubmed'}), StringElement('S0013-9351(83)71124-2', attributes={'IdType': 'pii'}), StringElement('10.1006/enrs.1993.1124', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8416117.\n",
      "[StringElement('8416117', attributes={'IdType': 'pubmed'}), StringElement('PMC1403434', attributes={'IdType': 'pmc'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8466495.\n",
      "[StringElement('8466495', attributes={'IdType': 'pubmed'}), StringElement('S0006-291X(83)71343-4', attributes={'IdType': 'pii'}), StringElement('10.1006/bbrc.1993.1343', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8520711.\n",
      "[StringElement('8520711', attributes={'IdType': 'pubmed'}), StringElement('1047-2797(94)00095-B', attributes={'IdType': 'pii'}), StringElement('10.1016/1047-2797(94)00095-b', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8598425.\n",
      "[StringElement('8598425', attributes={'IdType': 'pubmed'}), StringElement('10.1080/07315724.1995.10718553', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8604777.\n",
      "[StringElement('8604777', attributes={'IdType': 'pubmed'}), StringElement('PMC1380547', attributes={'IdType': 'pmc'}), StringElement('10.2105/ajph.86.4.480', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8610688.\n",
      "[StringElement('8610688', attributes={'IdType': 'pubmed'}), StringElement('10.1093/oxfordjournals.aje.a008816', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8611277.\n",
      "[StringElement('8611277', attributes={'IdType': 'pubmed'}), StringElement('S0894-7317(05)80001-X', attributes={'IdType': 'pii'}), StringElement('10.1016/s0894-7317(05)80001-x', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8611278.\n",
      "[StringElement('8611278', attributes={'IdType': 'pubmed'}), StringElement('S0894-7317(05)80002-1', attributes={'IdType': 'pii'}), StringElement('10.1016/s0894-7317(05)80002-1', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8616942.\n",
      "[StringElement('8616942', attributes={'IdType': 'pubmed'}), StringElement('10.1161/01.cir.93.1.60', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8633619.\n",
      "[StringElement('8633619', attributes={'IdType': 'pubmed'}), StringElement('10.1093/oxfordjournals.aje.a008749', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8686692.\n",
      "[StringElement('8686692', attributes={'IdType': 'pubmed'}), StringElement('10.1093/oxfordjournals.aje.a008918', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8686693.\n",
      "[StringElement('8686693', attributes={'IdType': 'pubmed'}), StringElement('10.1093/oxfordjournals.aje.a008919', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8727231.\n",
      "[StringElement('8727231', attributes={'IdType': 'pubmed'}), StringElement('10.1111/j.1530-0277.1996.tb01069.x', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8759809.\n",
      "[StringElement('8759809', attributes={'IdType': 'pubmed'}), StringElement('S0002914996002822', attributes={'IdType': 'pii'}), StringElement('10.1016/s0002-9149(96)00282-2', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8775596.\n",
      "[StringElement('8775596', attributes={'IdType': 'pubmed'}), StringElement('1047-2797(95)00135-2', attributes={'IdType': 'pii'}), StringElement('10.1016/1047-2797(95)00135-2', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8788322.\n",
      "[StringElement('8788322', attributes={'IdType': 'pubmed'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8827159.\n",
      "[StringElement('8827159', attributes={'IdType': 'pubmed'}), StringElement('1047279796000051', attributes={'IdType': 'pii'}), StringElement('10.1016/1047-2797(96)00005-1', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8827799.\n",
      "[StringElement('8827799', attributes={'IdType': 'pubmed'}), StringElement('10.1097/00006842-199607000-00009', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8876504.\n",
      "[StringElement('8876504', attributes={'IdType': 'pubmed'}), StringElement('PMC1380646', attributes={'IdType': 'pmc'}), StringElement('10.2105/ajph.86.10.1370', attributes={'IdType': 'doi'})]\n",
      "------------\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Retrieving DOI from PMID8879349.\n",
      "[StringElement('8879349', attributes={'IdType': 'pubmed'}), StringElement('S0895706196001495', attributes={'IdType': 'pii'}), StringElement('10.1016/s0895-7061(96)00149-5', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID8946271.\n",
      "[StringElement('8946271', attributes={'IdType': 'pubmed'}), StringElement('10.1177/174182679600300410', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID9003130.\n",
      "[StringElement('9003130', attributes={'IdType': 'pubmed'}), StringElement('PMC1380726', attributes={'IdType': 'pmc'}), StringElement('10.2105/ajph.86.12.1736', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID9006307.\n",
      "[StringElement('9006307', attributes={'IdType': 'pubmed'}), StringElement('10.1093/oxfordjournals.aje.a009081', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID9012637.\n",
      "[StringElement('9012637', attributes={'IdType': 'pubmed'}), StringElement('10.1161/01.atv.17.1.51', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID9017509.\n",
      "[StringElement('9017509', attributes={'IdType': 'pubmed'})]\n",
      "------------\n",
      "Retrieving DOI from PMID9024231.\n",
      "[StringElement('9024231', attributes={'IdType': 'pubmed'}), StringElement('10.1210/jcem.82.2.3732', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID9031018.\n",
      "[StringElement('9031018', attributes={'IdType': 'pubmed'}), StringElement('10.2190/HPB8-5M2N-VK6X-0FWN', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID9146443.\n",
      "[StringElement('9146443', attributes={'IdType': 'pubmed'}), StringElement('PMC1380844', attributes={'IdType': 'pmc'}), StringElement('10.2105/ajph.87.4.629', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID9146444.\n",
      "[StringElement('9146444', attributes={'IdType': 'pubmed'}), StringElement('PMC1380845', attributes={'IdType': 'pmc'}), StringElement('10.2105/ajph.87.4.635', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID9245672.\n",
      "[StringElement('9245672', attributes={'IdType': 'pubmed'}), StringElement('S0091743597901511', attributes={'IdType': 'pii'}), StringElement('10.1006/pmed.1997.0151', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID9286933.\n",
      "[StringElement('9286933', attributes={'IdType': 'pubmed'}), StringElement('10.1161/01.cir.96.4.1082', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID9308507.\n",
      "[StringElement('9308507', attributes={'IdType': 'pubmed'})]\n",
      "------------\n",
      "Retrieving DOI from PMID9321742.\n",
      "[StringElement('9321742', attributes={'IdType': 'pubmed'}), StringElement('10.1097/00004872-199715090-00005', attributes={'IdType': 'doi'})]\n",
      "------------\n",
      "Retrieving DOI from PMID9326433.\n",
      "[StringElement('9326433', attributes={'IdType': 'pubmed'}), StringElement('10.1093/oxfordjournals.aje.a009314', attributes={'IdType': 'doi'})]\n",
      "------------\n"
     ]
    },
    {
     "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>PMID</th>\n",
       "      <th>DOI</th>\n",
       "      <th>PMCID</th>\n",
       "      <th>DOI2</th>\n",
       "      <th>PMCID2</th>\n",
       "      <th>PMCID3</th>\n",
       "      <th>DOI3</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1315666</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>0197-2456(92)90031-T</td>\n",
       "      <td>none</td>\n",
       "      <td>none</td>\n",
       "      <td>10.1016/0197-2456(92)90031-t</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>1316830</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>0197-2456(92)90021-Q</td>\n",
       "      <td>none</td>\n",
       "      <td>none</td>\n",
       "      <td>10.1016/0197-2456(92)90021-q</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>1415137</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>10.1093/oxfordjournals.aje.a116480</td>\n",
       "      <td>none</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>1456336</td>\n",
       "      <td></td>\n",
       "      <td>1694535</td>\n",
       "      <td>10.1093/oxfordjournals.aje.a116480</td>\n",
       "      <td>PMC1694535</td>\n",
       "      <td>none</td>\n",
       "      <td>10.2105/ajph.82.12.1621</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1519841</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>10.1164/ajrccm/146.3.644</td>\n",
       "      <td>none</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>94</th>\n",
       "      <td>9245672</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>S0091743597901511</td>\n",
       "      <td>none</td>\n",
       "      <td>none</td>\n",
       "      <td>10.1006/pmed.1997.0151</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>95</th>\n",
       "      <td>9286933</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>10.1161/01.cir.96.4.1082</td>\n",
       "      <td>none</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>96</th>\n",
       "      <td>9308507</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>97</th>\n",
       "      <td>9321742</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>10.1097/00004872-199715090-00005</td>\n",
       "      <td>none</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>98</th>\n",
       "      <td>9326433</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>10.1093/oxfordjournals.aje.a009314</td>\n",
       "      <td>none</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>99 rows × 7 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       PMID DOI    PMCID                                DOI2      PMCID2  \\\n",
       "0   1315666                             0197-2456(92)90031-T        none   \n",
       "1   1316830                             0197-2456(92)90021-Q        none   \n",
       "2   1415137               10.1093/oxfordjournals.aje.a116480        none   \n",
       "3   1456336      1694535  10.1093/oxfordjournals.aje.a116480  PMC1694535   \n",
       "4   1519841                         10.1164/ajrccm/146.3.644        none   \n",
       "..      ...  ..      ...                                 ...         ...   \n",
       "94  9245672                                S0091743597901511        none   \n",
       "95  9286933                         10.1161/01.cir.96.4.1082        none   \n",
       "96  9308507                                                                \n",
       "97  9321742                 10.1097/00004872-199715090-00005        none   \n",
       "98  9326433               10.1093/oxfordjournals.aje.a009314        none   \n",
       "\n",
       "   PMCID3                          DOI3  \n",
       "0    none  10.1016/0197-2456(92)90031-t  \n",
       "1    none  10.1016/0197-2456(92)90021-q  \n",
       "2                                        \n",
       "3    none       10.2105/ajph.82.12.1621  \n",
       "4                                        \n",
       "..    ...                           ...  \n",
       "94   none        10.1006/pmed.1997.0151  \n",
       "95                                       \n",
       "96                                       \n",
       "97                                       \n",
       "98                                       \n",
       "\n",
       "[99 rows x 7 columns]"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# #####################################################\n",
    "# ## Get PMCID from PMID using Biopython ENTREZ READ\n",
    "# #####################################################\n",
    "\n",
    "# # Use iterrows to iterate through pandas pmid_list dataframe\n",
    "# for index, row in pmid_list.iterrows():\n",
    "\n",
    "#     PMID = row[\"PMID\"]\n",
    "#     api_key = \"9f4f75f5531d495aa2df93ea54696b607b08\"\n",
    "#     Entrez.email = \"karen.gutzman@northwestern.edu\"\n",
    "#     handle = Entrez.efetch(db=\"pubmed\", id=PMID, api_key=api_key, retmode=\"xml\")\n",
    "#     records = Entrez.read(handle)\n",
    "# #     ID_dict = {}\n",
    "# #     PMCID2= 'none'\n",
    "# #     PMCID3 = 'none'\n",
    "#     try:\n",
    "#         print(f\"Retrieving DOI from PMID{PMID}.\") \n",
    "#         #for item in records:\n",
    "#             # each record is a Python dictionary or list.\n",
    "#         ArtID2 = records[\"PubmedArticle\"][0]['PubmedData']['ArticleIdList']\n",
    "#         print(ArtID2)\n",
    "# #         PMCSTART = \"P\"\n",
    "# #         using list comprehension + startswith() + lower() \n",
    "# #         Words starting with specific letter \n",
    "       \n",
    "# #         if ArtID2.lower().startswith(PMCSTART.lower()):\n",
    "# #             PMCID2 = ArtID2\n",
    "# #             print(PMCID2)\n",
    "# #         else:\n",
    "# #             DOI2 =ArtID2\n",
    "# #             print(DOI2)\n",
    "        \n",
    "        \n",
    "# #         ## Add DOI to the PMID_List file in a new column called DOI\n",
    "# #         pmid_list.loc[index, 'DOI2'] = DOI2\n",
    "# #         pmid_list.loc[index, 'PMCID2'] = PMCID2\n",
    "        \n",
    "# #         ArtID3 = records[\"PubmedArticle\"][0]['PubmedData']['ArticleIdList'][2]\n",
    "        \n",
    "# #         if ArtID3.lower().startswith(PMCSTART.lower()):\n",
    "# #             PMCID3 = ArtID3\n",
    "# #             print(PMCID2)\n",
    "# #         else:\n",
    "# #             DOI3 =ArtID3\n",
    "# #             print(DOI3)\n",
    "        \n",
    "        \n",
    "# #         ## Add DOI to the PMID_List file in a new column called DOI\n",
    "# #         pmid_list.loc[index, 'DOI3'] = DOI3\n",
    "# #         pmid_list.loc[index, 'PMCID3'] = PMCID3\n",
    "                       \n",
    "    \n",
    "#     except (KeyError, IndexError):\n",
    "#         print(\"Missing field/result... skipping.\")\n",
    "        \n",
    "#     print(\"------------\")\n",
    "    \n",
    "    \n",
    "# handle.close()    \n",
    "# pmid_list"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.7.0"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}