DrugBank-MedDRA_Integration.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Parse the DrugBank XML and extract TSVs"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Run using Python 3 to avoid a non-ascii character error when writing to file with the csv module."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import csv\n",
    "import gzip\n",
    "import collections\n",
    "import re\n",
    "import io\n",
    "import json\n",
    "import xml.etree.ElementTree as ET\n",
    "\n",
    "import requests\n",
    "import pandas\n",
    "import numpy as np"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "import gseapy as gp\n",
    "from gseapy.parser import Biomart"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "bm = Biomart(verbose=False, host=\"asia.ensembl.org\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "xml_path = os.path.join('drugbank/', 'full database.xml')\n",
    "with open(xml_path) as xml_file:\n",
    "    tree = ET.parse(xml_file)\n",
    "root = tree.getroot()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "ns = '{http://www.drugbank.ca}'\n",
    "inchikey_template = \"{ns}calculated-properties/{ns}property[{ns}kind='InChIKey']/{ns}value\"\n",
    "inchi_template = \"{ns}calculated-properties/{ns}property[{ns}kind='InChI']/{ns}value\"\n",
    "\n",
    "rows = list()\n",
    "for i, drug in enumerate(root):\n",
    "    row = collections.OrderedDict()\n",
    "    assert drug.tag == ns + 'drug'\n",
    "    row['type'] = drug.get('type')\n",
    "    row['drugbank_id'] = drug.findtext(ns + \"drugbank-id[@primary='true']\")\n",
    "    row['name'] = drug.findtext(ns + \"name\")\n",
    "    row['description'] = drug.findtext(ns + \"description\")\n",
    "    row['groups'] = [group.text for group in\n",
    "        drug.findall(\"{ns}groups/{ns}group\".format(ns = ns))]\n",
    "    row['atc_codes'] = [code.get('code') for code in\n",
    "        drug.findall(\"{ns}atc-codes/{ns}atc-code\".format(ns = ns))]\n",
    "    row['categories'] = [x.findtext(ns + 'category') for x in\n",
    "        drug.findall(\"{ns}categories/{ns}category\".format(ns = ns))]\n",
    "    row['inchi'] = drug.findtext(inchi_template.format(ns = ns))\n",
    "    row['inchikey'] = drug.findtext(inchikey_template.format(ns = ns))\n",
    "    \n",
    "    # Add drug aliases\n",
    "    aliases = {\n",
    "        elem.text for elem in \n",
    "        drug.findall(\"{ns}international-brands/{ns}international-brand\".format(ns = ns)) +\n",
    "        drug.findall(\"{ns}synonyms/{ns}synonym[@language='English']\".format(ns = ns)) +\n",
    "        drug.findall(\"{ns}international-brands/{ns}international-brand\".format(ns = ns)) +\n",
    "        drug.findall(\"{ns}products/{ns}product/{ns}name\".format(ns = ns))\n",
    "\n",
    "    }\n",
    "    aliases.add(row['name'])\n",
    "    row['aliases'] = sorted(aliases)\n",
    "\n",
    "    rows.append(row)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "alias_dict = {row['drugbank_id']: row['aliases'] for row in rows}\n",
    "with open('./drugbank/data/aliases.json', 'w') as fp:\n",
    "    json.dump(alias_dict, fp, indent=2, sort_keys=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "def collapse_list_values(row):\n",
    "    for key, value in row.items():\n",
    "        if isinstance(value, list):\n",
    "            row[key] = '|'.join(value)\n",
    "    return row\n",
    "\n",
    "rows = list(map(collapse_list_values, rows))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>drugbank_id</th>\n",
       "      <th>name</th>\n",
       "      <th>type</th>\n",
       "      <th>groups</th>\n",
       "      <th>atc_codes</th>\n",
       "      <th>categories</th>\n",
       "      <th>inchikey</th>\n",
       "      <th>inchi</th>\n",
       "      <th>description</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>DB00001</td>\n",
       "      <td>Lepirudin</td>\n",
       "      <td>biotech</td>\n",
       "      <td>approved</td>\n",
       "      <td>B01AE02</td>\n",
       "      <td>Amino Acids, Peptides, and Proteins|Anticoagul...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>Lepirudin is identical to natural hirudin exce...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>DB00002</td>\n",
       "      <td>Cetuximab</td>\n",
       "      <td>biotech</td>\n",
       "      <td>approved</td>\n",
       "      <td>L01XC06</td>\n",
       "      <td>Amino Acids, Peptides, and Proteins|Antibodies...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>Cetuximab is an epidermal growth factor recept...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>DB00003</td>\n",
       "      <td>Dornase alfa</td>\n",
       "      <td>biotech</td>\n",
       "      <td>approved</td>\n",
       "      <td>R05CB13</td>\n",
       "      <td>Amino Acids, Peptides, and Proteins|Cough and ...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>Dornase alfa is a biosynthetic form of human d...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>DB00004</td>\n",
       "      <td>Denileukin diftitox</td>\n",
       "      <td>biotech</td>\n",
       "      <td>approved|investigational</td>\n",
       "      <td>L01XX29</td>\n",
       "      <td>ADP Ribose Transferases|Amino Acids, Peptides,...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>A recombinant DNA-derived cytotoxic protein co...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>DB00005</td>\n",
       "      <td>Etanercept</td>\n",
       "      <td>biotech</td>\n",
       "      <td>approved|investigational</td>\n",
       "      <td>L04AB01</td>\n",
       "      <td>Agents reducing cytokine levels|Amino Acids, P...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>Dimeric fusion protein consisting of the extra...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  drugbank_id                 name     type                    groups  \\\n",
       "0     DB00001            Lepirudin  biotech                  approved   \n",
       "1     DB00002            Cetuximab  biotech                  approved   \n",
       "2     DB00003         Dornase alfa  biotech                  approved   \n",
       "3     DB00004  Denileukin diftitox  biotech  approved|investigational   \n",
       "4     DB00005           Etanercept  biotech  approved|investigational   \n",
       "\n",
       "  atc_codes                                         categories inchikey inchi  \\\n",
       "0   B01AE02  Amino Acids, Peptides, and Proteins|Anticoagul...     None  None   \n",
       "1   L01XC06  Amino Acids, Peptides, and Proteins|Antibodies...     None  None   \n",
       "2   R05CB13  Amino Acids, Peptides, and Proteins|Cough and ...     None  None   \n",
       "3   L01XX29  ADP Ribose Transferases|Amino Acids, Peptides,...     None  None   \n",
       "4   L04AB01  Agents reducing cytokine levels|Amino Acids, P...     None  None   \n",
       "\n",
       "                                         description  \n",
       "0  Lepirudin is identical to natural hirudin exce...  \n",
       "1  Cetuximab is an epidermal growth factor recept...  \n",
       "2  Dornase alfa is a biosynthetic form of human d...  \n",
       "3  A recombinant DNA-derived cytotoxic protein co...  \n",
       "4  Dimeric fusion protein consisting of the extra...  "
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "columns = ['drugbank_id', 'name', 'type', 'groups', 'atc_codes', 'categories', 'inchikey', 'inchi', 'description']\n",
    "drugbank_df = pandas.DataFrame.from_dict(rows)[columns]\n",
    "drugbank_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(13563, 9)"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "drugbank_df.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
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       "\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>drugbank_id</th>\n",
       "      <th>name</th>\n",
       "      <th>type</th>\n",
       "      <th>groups</th>\n",
       "      <th>atc_codes</th>\n",
       "      <th>categories</th>\n",
       "      <th>inchikey</th>\n",
       "      <th>inchi</th>\n",
       "      <th>description</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>DB00006</td>\n",
       "      <td>Bivalirudin</td>\n",
       "      <td>small molecule</td>\n",
       "      <td>approved|investigational</td>\n",
       "      <td>B01AE06</td>\n",
       "      <td>Amino Acids, Peptides, and Proteins|Anticoagul...</td>\n",
       "      <td>OIRCOABEOLEUMC-GEJPAHFPSA-N</td>\n",
       "      <td>InChI=1S/C98H138N24O33/c1-5-52(4)82(96(153)122...</td>\n",
       "      <td>Bivalirudin is a synthetic 20 residue peptide ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>DB00007</td>\n",
       "      <td>Leuprolide</td>\n",
       "      <td>small molecule</td>\n",
       "      <td>approved|investigational</td>\n",
       "      <td>L02AE51|L02AE02</td>\n",
       "      <td>Adrenal Cortex Hormones|Agents Causing Muscle ...</td>\n",
       "      <td>GFIJNRVAKGFPGQ-LIJARHBVSA-N</td>\n",
       "      <td>InChI=1S/C59H84N16O12/c1-6-63-57(86)48-14-10-2...</td>\n",
       "      <td>Leuprolide belongs to the general class of dru...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>DB00014</td>\n",
       "      <td>Goserelin</td>\n",
       "      <td>small molecule</td>\n",
       "      <td>approved</td>\n",
       "      <td>L02AE03</td>\n",
       "      <td>Adrenal Cortex Hormones|Amino Acids, Peptides,...</td>\n",
       "      <td>BLCLNMBMMGCOAS-URPVMXJPSA-N</td>\n",
       "      <td>InChI=1S/C59H84N18O14/c1-31(2)22-40(49(82)68-3...</td>\n",
       "      <td>Goserelin is a synthetic hormone. In men, it s...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>DB00027</td>\n",
       "      <td>Gramicidin D</td>\n",
       "      <td>small molecule</td>\n",
       "      <td>approved</td>\n",
       "      <td>R02AB30</td>\n",
       "      <td>Amino Acids, Peptides, and Proteins|Anti-Bacte...</td>\n",
       "      <td>NDAYQJDHGXTBJL-MWWSRJDJSA-N</td>\n",
       "      <td>InChI=1S/C96H135N19O16/c1-50(2)36-71(105-79(11...</td>\n",
       "      <td>Gramcidin D is a heterogeneous mixture of thre...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>33</th>\n",
       "      <td>DB00035</td>\n",
       "      <td>Desmopressin</td>\n",
       "      <td>small molecule</td>\n",
       "      <td>approved</td>\n",
       "      <td>H01BA02</td>\n",
       "      <td>Agents that produce hypertension|Amino Acids, ...</td>\n",
       "      <td>NFLWUMRGJYTJIN-PNIOQBSNSA-N</td>\n",
       "      <td>InChI=1S/C46H64N14O12S2/c47-35(62)15-14-29-40(...</td>\n",
       "      <td>Desmopressin (dDAVP), a synthetic analogue of ...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   drugbank_id          name            type                    groups  \\\n",
       "5      DB00006   Bivalirudin  small molecule  approved|investigational   \n",
       "6      DB00007    Leuprolide  small molecule  approved|investigational   \n",
       "13     DB00014     Goserelin  small molecule                  approved   \n",
       "25     DB00027  Gramicidin D  small molecule                  approved   \n",
       "33     DB00035  Desmopressin  small molecule                  approved   \n",
       "\n",
       "          atc_codes                                         categories  \\\n",
       "5           B01AE06  Amino Acids, Peptides, and Proteins|Anticoagul...   \n",
       "6   L02AE51|L02AE02  Adrenal Cortex Hormones|Agents Causing Muscle ...   \n",
       "13          L02AE03  Adrenal Cortex Hormones|Amino Acids, Peptides,...   \n",
       "25          R02AB30  Amino Acids, Peptides, and Proteins|Anti-Bacte...   \n",
       "33          H01BA02  Agents that produce hypertension|Amino Acids, ...   \n",
       "\n",
       "                       inchikey  \\\n",
       "5   OIRCOABEOLEUMC-GEJPAHFPSA-N   \n",
       "6   GFIJNRVAKGFPGQ-LIJARHBVSA-N   \n",
       "13  BLCLNMBMMGCOAS-URPVMXJPSA-N   \n",
       "25  NDAYQJDHGXTBJL-MWWSRJDJSA-N   \n",
       "33  NFLWUMRGJYTJIN-PNIOQBSNSA-N   \n",
       "\n",
       "                                                inchi  \\\n",
       "5   InChI=1S/C98H138N24O33/c1-5-52(4)82(96(153)122...   \n",
       "6   InChI=1S/C59H84N16O12/c1-6-63-57(86)48-14-10-2...   \n",
       "13  InChI=1S/C59H84N18O14/c1-31(2)22-40(49(82)68-3...   \n",
       "25  InChI=1S/C96H135N19O16/c1-50(2)36-71(105-79(11...   \n",
       "33  InChI=1S/C46H64N14O12S2/c47-35(62)15-14-29-40(...   \n",
       "\n",
       "                                          description  \n",
       "5   Bivalirudin is a synthetic 20 residue peptide ...  \n",
       "6   Leuprolide belongs to the general class of dru...  \n",
       "13  Goserelin is a synthetic hormone. In men, it s...  \n",
       "25  Gramcidin D is a heterogeneous mixture of thre...  \n",
       "33  Desmopressin (dDAVP), a synthetic analogue of ...  "
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "drugbank_slim_df = drugbank_df[\n",
    "    drugbank_df.groups.map(lambda x: 'approved' in x) &\n",
    "    drugbank_df.inchi.map(lambda x: x is not None) &\n",
    "    drugbank_df.type.map(lambda x: x == 'small molecule')\n",
    "]\n",
    "drugbank_slim_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(2618, 9)"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "drugbank_slim_df.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "# write drugbank tsv\n",
    "path = os.path.join('drugbank/data', 'drugbank.tsv')\n",
    "drugbank_df.to_csv(path, sep='\\t', index=False)\n",
    "\n",
    "# write slim drugbank tsv\n",
    "path = os.path.join('drugbank/data', 'drugbank-slim.tsv')\n",
    "drugbank_slim_df.to_csv(path, sep='\\t', index=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Extract protein information"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "protein_rows = list()\n",
    "for i, drug in enumerate(root):\n",
    "    drugbank_id = drug.findtext(ns + \"drugbank-id[@primary='true']\")\n",
    "    for category in ['target', 'enzyme', 'carrier', 'transporter']:\n",
    "        proteins = drug.findall('{ns}{cat}s/{ns}{cat}'.format(ns=ns, cat=category))\n",
    "        for protein in proteins:\n",
    "            row = {'drugbank_id': drugbank_id, 'category': category}\n",
    "            row['organism'] = protein.findtext('{}organism'.format(ns))\n",
    "            row['known_action'] = protein.findtext('{}known-action'.format(ns))\n",
    "            actions = protein.findall('{ns}actions/{ns}action'.format(ns=ns))\n",
    "            row['actions'] = '|'.join(action.text for action in actions)\n",
    "            uniprot_ids = [polypep.text for polypep in protein.findall(\n",
    "                \"{ns}polypeptide/{ns}external-identifiers/{ns}external-identifier[{ns}resource='UniProtKB']/{ns}identifier\".format(ns=ns))]            \n",
    "            if len(uniprot_ids) != 1:\n",
    "                continue\n",
    "            row['uniprot_id'] = uniprot_ids[0]\n",
    "            ref_text = protein.findtext(\"{ns}references[@format='textile']\".format(ns=ns))\n",
    "            if str(type(ref_text)) != \"<class 'NoneType'>\" :\n",
    "                pmids = re.findall(r'pubmed/([0-9]+)', ref_text)\n",
    "                row['pubmed_ids'] = '|'.join(pmids)\n",
    "            else:\n",
    "                row['pubmed_ids'] = None\n",
    "            protein_rows.append(row)\n",
    "\n",
    "protein_df = pandas.DataFrame.from_dict(protein_rows)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Read our uniprot to entrez_gene mapping\n",
    "response = requests.get('http://git.dhimmel.com/uniprot/data/map/GeneID.tsv.gz', stream=True)\n",
    "text = io.TextIOWrapper(gzip.GzipFile(fileobj=response.raw))\n",
    "uniprot_df = pandas.read_table(text, engine='python')\n",
    "uniprot_df.rename(columns={'uniprot': 'uniprot_id', 'GeneID': 'entrez_gene_id'}, inplace=True)\n",
    "\n",
    "# merge uniprot mapping with protein_df\n",
    "entrez_df = protein_df.merge(uniprot_df, how='inner')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "columns = ['drugbank_id', 'category', 'uniprot_id', 'entrez_gene_id', 'organism',\n",
    "           'known_action', 'actions', 'pubmed_ids']\n",
    "entrez_df = entrez_df[columns]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [],
   "source": [
    "path = os.path.join('drugbank/data', 'proteins.tsv')\n",
    "entrez_df.to_csv(path, sep='\\t', index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "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>drugbank_id</th>\n",
       "      <th>category</th>\n",
       "      <th>uniprot_id</th>\n",
       "      <th>entrez_gene_id</th>\n",
       "      <th>organism</th>\n",
       "      <th>known_action</th>\n",
       "      <th>actions</th>\n",
       "      <th>pubmed_ids</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>DB00001</td>\n",
       "      <td>target</td>\n",
       "      <td>P00734</td>\n",
       "      <td>2147</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>inhibitor</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>DB00006</td>\n",
       "      <td>target</td>\n",
       "      <td>P00734</td>\n",
       "      <td>2147</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>inhibitor</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>DB00025</td>\n",
       "      <td>enzyme</td>\n",
       "      <td>P00734</td>\n",
       "      <td>2147</td>\n",
       "      <td>Humans</td>\n",
       "      <td>unknown</td>\n",
       "      <td>activator</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>DB00055</td>\n",
       "      <td>target</td>\n",
       "      <td>P00734</td>\n",
       "      <td>2147</td>\n",
       "      <td>Humans</td>\n",
       "      <td>unknown</td>\n",
       "      <td></td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>DB00100</td>\n",
       "      <td>target</td>\n",
       "      <td>P00734</td>\n",
       "      <td>2147</td>\n",
       "      <td>Humans</td>\n",
       "      <td>unknown</td>\n",
       "      <td></td>\n",
       "      <td>None</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",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27322</th>\n",
       "      <td>DB15493</td>\n",
       "      <td>target</td>\n",
       "      <td>Q8IXJ6</td>\n",
       "      <td>22933</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>inhibitor</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27323</th>\n",
       "      <td>DB15495</td>\n",
       "      <td>target</td>\n",
       "      <td>P35232</td>\n",
       "      <td>5245</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>inhibitor</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27324</th>\n",
       "      <td>DB15496</td>\n",
       "      <td>target</td>\n",
       "      <td>P35232</td>\n",
       "      <td>5245</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>inhibitor</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27325</th>\n",
       "      <td>DB15570</td>\n",
       "      <td>target</td>\n",
       "      <td>P51679</td>\n",
       "      <td>1233</td>\n",
       "      <td>Humans</td>\n",
       "      <td>unknown</td>\n",
       "      <td>antagonist</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27326</th>\n",
       "      <td>DB15593</td>\n",
       "      <td>target</td>\n",
       "      <td>P11532</td>\n",
       "      <td>1756</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>inducer</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>27327 rows × 8 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      drugbank_id category uniprot_id  entrez_gene_id organism known_action  \\\n",
       "0         DB00001   target     P00734            2147   Humans          yes   \n",
       "1         DB00006   target     P00734            2147   Humans          yes   \n",
       "2         DB00025   enzyme     P00734            2147   Humans      unknown   \n",
       "3         DB00055   target     P00734            2147   Humans      unknown   \n",
       "4         DB00100   target     P00734            2147   Humans      unknown   \n",
       "...           ...      ...        ...             ...      ...          ...   \n",
       "27322     DB15493   target     Q8IXJ6           22933   Humans          yes   \n",
       "27323     DB15495   target     P35232            5245   Humans          yes   \n",
       "27324     DB15496   target     P35232            5245   Humans          yes   \n",
       "27325     DB15570   target     P51679            1233   Humans      unknown   \n",
       "27326     DB15593   target     P11532            1756   Humans          yes   \n",
       "\n",
       "          actions pubmed_ids  \n",
       "0       inhibitor       None  \n",
       "1       inhibitor       None  \n",
       "2       activator       None  \n",
       "3                       None  \n",
       "4                       None  \n",
       "...           ...        ...  \n",
       "27322   inhibitor       None  \n",
       "27323   inhibitor       None  \n",
       "27324   inhibitor       None  \n",
       "27325  antagonist       None  \n",
       "27326     inducer       None  \n",
       "\n",
       "[27327 rows x 8 columns]"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "entrez_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "                                              11195\n",
       "inhibitor                                      5042\n",
       "substrate                                      4145\n",
       "antagonist                                     1564\n",
       "agonist                                        1101\n",
       "                                              ...  \n",
       "binder|potentiator                                1\n",
       "intercalation                                     1\n",
       "desensitize the target                            1\n",
       "antagonist|inhibitory allosteric modulator        1\n",
       "inducer|acetylation                               1\n",
       "Name: actions, Length: 112, dtype: int64"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "entrez_df.actions.value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "4628"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Number of unique genes with an interaction\n",
    "len(set(entrez_df.entrez_gene_id))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "7057"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Number of unique drugs  with an interaction\n",
    "len(set(entrez_df.drugbank_id))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
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       "    }\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>drugbank_id</th>\n",
       "      <th>name</th>\n",
       "      <th>type</th>\n",
       "      <th>groups</th>\n",
       "      <th>atc_codes</th>\n",
       "      <th>categories</th>\n",
       "      <th>inchikey</th>\n",
       "      <th>inchi</th>\n",
       "      <th>description</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>DB00001</td>\n",
       "      <td>Lepirudin</td>\n",
       "      <td>biotech</td>\n",
       "      <td>approved</td>\n",
       "      <td>B01AE02</td>\n",
       "      <td>Amino Acids, Peptides, and Proteins|Anticoagul...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>Lepirudin is identical to natural hirudin exce...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>DB00002</td>\n",
       "      <td>Cetuximab</td>\n",
       "      <td>biotech</td>\n",
       "      <td>approved</td>\n",
       "      <td>L01XC06</td>\n",
       "      <td>Amino Acids, Peptides, and Proteins|Antibodies...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>Cetuximab is an epidermal growth factor recept...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>DB00003</td>\n",
       "      <td>Dornase alfa</td>\n",
       "      <td>biotech</td>\n",
       "      <td>approved</td>\n",
       "      <td>R05CB13</td>\n",
       "      <td>Amino Acids, Peptides, and Proteins|Cough and ...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>Dornase alfa is a biosynthetic form of human d...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>DB00004</td>\n",
       "      <td>Denileukin diftitox</td>\n",
       "      <td>biotech</td>\n",
       "      <td>approved|investigational</td>\n",
       "      <td>L01XX29</td>\n",
       "      <td>ADP Ribose Transferases|Amino Acids, Peptides,...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>A recombinant DNA-derived cytotoxic protein co...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>DB00005</td>\n",
       "      <td>Etanercept</td>\n",
       "      <td>biotech</td>\n",
       "      <td>approved|investigational</td>\n",
       "      <td>L04AB01</td>\n",
       "      <td>Agents reducing cytokine levels|Amino Acids, P...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>Dimeric fusion protein consisting of the extra...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  drugbank_id                 name     type                    groups  \\\n",
       "0     DB00001            Lepirudin  biotech                  approved   \n",
       "1     DB00002            Cetuximab  biotech                  approved   \n",
       "2     DB00003         Dornase alfa  biotech                  approved   \n",
       "3     DB00004  Denileukin diftitox  biotech  approved|investigational   \n",
       "4     DB00005           Etanercept  biotech  approved|investigational   \n",
       "\n",
       "  atc_codes                                         categories inchikey inchi  \\\n",
       "0   B01AE02  Amino Acids, Peptides, and Proteins|Anticoagul...     None  None   \n",
       "1   L01XC06  Amino Acids, Peptides, and Proteins|Antibodies...     None  None   \n",
       "2   R05CB13  Amino Acids, Peptides, and Proteins|Cough and ...     None  None   \n",
       "3   L01XX29  ADP Ribose Transferases|Amino Acids, Peptides,...     None  None   \n",
       "4   L04AB01  Agents reducing cytokine levels|Amino Acids, P...     None  None   \n",
       "\n",
       "                                         description  \n",
       "0  Lepirudin is identical to natural hirudin exce...  \n",
       "1  Cetuximab is an epidermal growth factor recept...  \n",
       "2  Dornase alfa is a biosynthetic form of human d...  \n",
       "3  A recombinant DNA-derived cytotoxic protein co...  \n",
       "4  Dimeric fusion protein consisting of the extra...  "
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "drugbank_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Index(['drugbank_id', 'name', 'type', 'groups', 'atc_codes', 'categories',\n",
       "       'inchikey', 'inchi', 'description'],\n",
       "      dtype='object')"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "drugbank_df.columns"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Maping multiple columns\n",
    "drugbank_df.index = drugbank_df.drugbank_id\n",
    "entrez_df.index = entrez_df.drugbank_id\n",
    "for i in ['name', 'type', 'groups', 'atc_codes', 'categories', 'description']:\n",
    "    entrez_df[i] = entrez_df.drugbank_id.map(drugbank_df[i])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>drugbank_id</th>\n",
       "      <th>category</th>\n",
       "      <th>uniprot_id</th>\n",
       "      <th>entrez_gene_id</th>\n",
       "      <th>organism</th>\n",
       "      <th>known_action</th>\n",
       "      <th>actions</th>\n",
       "      <th>pubmed_ids</th>\n",
       "      <th>name</th>\n",
       "      <th>type</th>\n",
       "      <th>groups</th>\n",
       "      <th>atc_codes</th>\n",
       "      <th>categories</th>\n",
       "      <th>description</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>drugbank_id</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>DB00001</th>\n",
       "      <td>DB00001</td>\n",
       "      <td>target</td>\n",
       "      <td>P00734</td>\n",
       "      <td>2147</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>inhibitor</td>\n",
       "      <td>None</td>\n",
       "      <td>Lepirudin</td>\n",
       "      <td>biotech</td>\n",
       "      <td>approved</td>\n",
       "      <td>B01AE02</td>\n",
       "      <td>Amino Acids, Peptides, and Proteins|Anticoagul...</td>\n",
       "      <td>Lepirudin is identical to natural hirudin exce...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB00006</th>\n",
       "      <td>DB00006</td>\n",
       "      <td>target</td>\n",
       "      <td>P00734</td>\n",
       "      <td>2147</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>inhibitor</td>\n",
       "      <td>None</td>\n",
       "      <td>Bivalirudin</td>\n",
       "      <td>small molecule</td>\n",
       "      <td>approved|investigational</td>\n",
       "      <td>B01AE06</td>\n",
       "      <td>Amino Acids, Peptides, and Proteins|Anticoagul...</td>\n",
       "      <td>Bivalirudin is a synthetic 20 residue peptide ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB00025</th>\n",
       "      <td>DB00025</td>\n",
       "      <td>enzyme</td>\n",
       "      <td>P00734</td>\n",
       "      <td>2147</td>\n",
       "      <td>Humans</td>\n",
       "      <td>unknown</td>\n",
       "      <td>activator</td>\n",
       "      <td>None</td>\n",
       "      <td>Antihemophilic factor, human recombinant</td>\n",
       "      <td>biotech</td>\n",
       "      <td>approved|investigational</td>\n",
       "      <td>B02BD02</td>\n",
       "      <td>Amino Acids, Peptides, and Proteins|Biological...</td>\n",
       "      <td>Human recombinant antihemophilic factor (AHF) ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB00055</th>\n",
       "      <td>DB00055</td>\n",
       "      <td>target</td>\n",
       "      <td>P00734</td>\n",
       "      <td>2147</td>\n",
       "      <td>Humans</td>\n",
       "      <td>unknown</td>\n",
       "      <td></td>\n",
       "      <td>None</td>\n",
       "      <td>Drotrecogin alfa</td>\n",
       "      <td>biotech</td>\n",
       "      <td>approved|investigational|withdrawn</td>\n",
       "      <td>B01AD10</td>\n",
       "      <td>Amino Acids, Peptides, and Proteins|Anti-Infec...</td>\n",
       "      <td>Drotrecogin alfa is activated human protein C ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB00100</th>\n",
       "      <td>DB00100</td>\n",
       "      <td>target</td>\n",
       "      <td>P00734</td>\n",
       "      <td>2147</td>\n",
       "      <td>Humans</td>\n",
       "      <td>unknown</td>\n",
       "      <td></td>\n",
       "      <td>None</td>\n",
       "      <td>Coagulation Factor IX (Recombinant)</td>\n",
       "      <td>biotech</td>\n",
       "      <td>approved|investigational</td>\n",
       "      <td></td>\n",
       "      <td>Blood Coagulation Factors|Hemostatics|Increase...</td>\n",
       "      <td>Recombinant Coagulation Factor IX is a purifie...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "            drugbank_id category uniprot_id  entrez_gene_id organism  \\\n",
       "drugbank_id                                                            \n",
       "DB00001         DB00001   target     P00734            2147   Humans   \n",
       "DB00006         DB00006   target     P00734            2147   Humans   \n",
       "DB00025         DB00025   enzyme     P00734            2147   Humans   \n",
       "DB00055         DB00055   target     P00734            2147   Humans   \n",
       "DB00100         DB00100   target     P00734            2147   Humans   \n",
       "\n",
       "            known_action    actions pubmed_ids  \\\n",
       "drugbank_id                                      \n",
       "DB00001              yes  inhibitor       None   \n",
       "DB00006              yes  inhibitor       None   \n",
       "DB00025          unknown  activator       None   \n",
       "DB00055          unknown                  None   \n",
       "DB00100          unknown                  None   \n",
       "\n",
       "                                                 name            type  \\\n",
       "drugbank_id                                                             \n",
       "DB00001                                     Lepirudin         biotech   \n",
       "DB00006                                   Bivalirudin  small molecule   \n",
       "DB00025      Antihemophilic factor, human recombinant         biotech   \n",
       "DB00055                              Drotrecogin alfa         biotech   \n",
       "DB00100           Coagulation Factor IX (Recombinant)         biotech   \n",
       "\n",
       "                                         groups atc_codes  \\\n",
       "drugbank_id                                                 \n",
       "DB00001                                approved   B01AE02   \n",
       "DB00006                approved|investigational   B01AE06   \n",
       "DB00025                approved|investigational   B02BD02   \n",
       "DB00055      approved|investigational|withdrawn   B01AD10   \n",
       "DB00100                approved|investigational             \n",
       "\n",
       "                                                    categories  \\\n",
       "drugbank_id                                                      \n",
       "DB00001      Amino Acids, Peptides, and Proteins|Anticoagul...   \n",
       "DB00006      Amino Acids, Peptides, and Proteins|Anticoagul...   \n",
       "DB00025      Amino Acids, Peptides, and Proteins|Biological...   \n",
       "DB00055      Amino Acids, Peptides, and Proteins|Anti-Infec...   \n",
       "DB00100      Blood Coagulation Factors|Hemostatics|Increase...   \n",
       "\n",
       "                                                   description  \n",
       "drugbank_id                                                     \n",
       "DB00001      Lepirudin is identical to natural hirudin exce...  \n",
       "DB00006      Bivalirudin is a synthetic 20 residue peptide ...  \n",
       "DB00025      Human recombinant antihemophilic factor (AHF) ...  \n",
       "DB00055      Drotrecogin alfa is activated human protein C ...  \n",
       "DB00100      Recombinant Coagulation Factor IX is a purifie...  "
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "entrez_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Mapping Entrez to gene symbol\n",
    "glist = np.unique(entrez_df.entrez_gene_id.values).tolist()\n",
    "glist = [str(x) for x in glist if type(x) ==int]\n",
    "results = bm.query(dataset='hsapiens_gene_ensembl', attributes=['entrezgene_id','hgnc_symbol'],#, 'go_id'],\n",
    "                   filters={'entrezgene_id': glist})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>drugbank_id</th>\n",
       "      <th>category</th>\n",
       "      <th>uniprot_id</th>\n",
       "      <th>entrez_gene_id</th>\n",
       "      <th>organism</th>\n",
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       "      <th>name</th>\n",
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       "      <th>atc_codes</th>\n",
       "      <th>categories</th>\n",
       "      <th>description</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>drugbank_id</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>DB00001</th>\n",
       "      <td>DB00001</td>\n",
       "      <td>target</td>\n",
       "      <td>P00734</td>\n",
       "      <td>2147</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>inhibitor</td>\n",
       "      <td>None</td>\n",
       "      <td>Lepirudin</td>\n",
       "      <td>biotech</td>\n",
       "      <td>approved</td>\n",
       "      <td>B01AE02</td>\n",
       "      <td>Amino Acids, Peptides, and Proteins|Anticoagul...</td>\n",
       "      <td>Lepirudin is identical to natural hirudin exce...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB00006</th>\n",
       "      <td>DB00006</td>\n",
       "      <td>target</td>\n",
       "      <td>P00734</td>\n",
       "      <td>2147</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>inhibitor</td>\n",
       "      <td>None</td>\n",
       "      <td>Bivalirudin</td>\n",
       "      <td>small molecule</td>\n",
       "      <td>approved|investigational</td>\n",
       "      <td>B01AE06</td>\n",
       "      <td>Amino Acids, Peptides, and Proteins|Anticoagul...</td>\n",
       "      <td>Bivalirudin is a synthetic 20 residue peptide ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB00025</th>\n",
       "      <td>DB00025</td>\n",
       "      <td>enzyme</td>\n",
       "      <td>P00734</td>\n",
       "      <td>2147</td>\n",
       "      <td>Humans</td>\n",
       "      <td>unknown</td>\n",
       "      <td>activator</td>\n",
       "      <td>None</td>\n",
       "      <td>Antihemophilic factor, human recombinant</td>\n",
       "      <td>biotech</td>\n",
       "      <td>approved|investigational</td>\n",
       "      <td>B02BD02</td>\n",
       "      <td>Amino Acids, Peptides, and Proteins|Biological...</td>\n",
       "      <td>Human recombinant antihemophilic factor (AHF) ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB00055</th>\n",
       "      <td>DB00055</td>\n",
       "      <td>target</td>\n",
       "      <td>P00734</td>\n",
       "      <td>2147</td>\n",
       "      <td>Humans</td>\n",
       "      <td>unknown</td>\n",
       "      <td></td>\n",
       "      <td>None</td>\n",
       "      <td>Drotrecogin alfa</td>\n",
       "      <td>biotech</td>\n",
       "      <td>approved|investigational|withdrawn</td>\n",
       "      <td>B01AD10</td>\n",
       "      <td>Amino Acids, Peptides, and Proteins|Anti-Infec...</td>\n",
       "      <td>Drotrecogin alfa is activated human protein C ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB00100</th>\n",
       "      <td>DB00100</td>\n",
       "      <td>target</td>\n",
       "      <td>P00734</td>\n",
       "      <td>2147</td>\n",
       "      <td>Humans</td>\n",
       "      <td>unknown</td>\n",
       "      <td></td>\n",
       "      <td>None</td>\n",
       "      <td>Coagulation Factor IX (Recombinant)</td>\n",
       "      <td>biotech</td>\n",
       "      <td>approved|investigational</td>\n",
       "      <td></td>\n",
       "      <td>Blood Coagulation Factors|Hemostatics|Increase...</td>\n",
       "      <td>Recombinant Coagulation Factor IX is a purifie...</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",
       "      <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>DB15493</th>\n",
       "      <td>DB15493</td>\n",
       "      <td>target</td>\n",
       "      <td>Q8IXJ6</td>\n",
       "      <td>22933</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>inhibitor</td>\n",
       "      <td>None</td>\n",
       "      <td>Cambinol</td>\n",
       "      <td>small molecule</td>\n",
       "      <td>experimental</td>\n",
       "      <td></td>\n",
       "      <td>Pyrimidines</td>\n",
       "      <td>Cambinol is a beta-naphtol derivative that inh...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB15495</th>\n",
       "      <td>DB15495</td>\n",
       "      <td>target</td>\n",
       "      <td>P35232</td>\n",
       "      <td>5245</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>inhibitor</td>\n",
       "      <td>None</td>\n",
       "      <td>Rocaglamide</td>\n",
       "      <td>small molecule</td>\n",
       "      <td>experimental</td>\n",
       "      <td></td>\n",
       "      <td>Heterocyclic Compounds, Fused-Ring</td>\n",
       "      <td>Rocaglamide, also referred to as rocaglamide-A...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB15496</th>\n",
       "      <td>DB15496</td>\n",
       "      <td>target</td>\n",
       "      <td>P35232</td>\n",
       "      <td>5245</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>inhibitor</td>\n",
       "      <td>None</td>\n",
       "      <td>Didesmethylrocaglamide</td>\n",
       "      <td>small molecule</td>\n",
       "      <td>experimental</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>Didesmethylrocaglamide is a naturally-occurrin...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB15570</th>\n",
       "      <td>DB15570</td>\n",
       "      <td>target</td>\n",
       "      <td>P51679</td>\n",
       "      <td>1233</td>\n",
       "      <td>Humans</td>\n",
       "      <td>unknown</td>\n",
       "      <td>antagonist</td>\n",
       "      <td>None</td>\n",
       "      <td>FLX475</td>\n",
       "      <td>small molecule</td>\n",
       "      <td>investigational</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>FLX475 is a small molecule CCR4 antagonist bei...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB15593</th>\n",
       "      <td>DB15593</td>\n",
       "      <td>target</td>\n",
       "      <td>P11532</td>\n",
       "      <td>1756</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>inducer</td>\n",
       "      <td>None</td>\n",
       "      <td>Golodirsen</td>\n",
       "      <td>biotech</td>\n",
       "      <td>approved</td>\n",
       "      <td></td>\n",
       "      <td>Drugs that are Mainly Renally Excreted|Oligonu...</td>\n",
       "      <td>Golodirsen is a morpholino antisense oligomer ...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>27327 rows × 14 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "            drugbank_id category uniprot_id  entrez_gene_id organism  \\\n",
       "drugbank_id                                                            \n",
       "DB00001         DB00001   target     P00734            2147   Humans   \n",
       "DB00006         DB00006   target     P00734            2147   Humans   \n",
       "DB00025         DB00025   enzyme     P00734            2147   Humans   \n",
       "DB00055         DB00055   target     P00734            2147   Humans   \n",
       "DB00100         DB00100   target     P00734            2147   Humans   \n",
       "...                 ...      ...        ...             ...      ...   \n",
       "DB15493         DB15493   target     Q8IXJ6           22933   Humans   \n",
       "DB15495         DB15495   target     P35232            5245   Humans   \n",
       "DB15496         DB15496   target     P35232            5245   Humans   \n",
       "DB15570         DB15570   target     P51679            1233   Humans   \n",
       "DB15593         DB15593   target     P11532            1756   Humans   \n",
       "\n",
       "            known_action     actions pubmed_ids  \\\n",
       "drugbank_id                                       \n",
       "DB00001              yes   inhibitor       None   \n",
       "DB00006              yes   inhibitor       None   \n",
       "DB00025          unknown   activator       None   \n",
       "DB00055          unknown                   None   \n",
       "DB00100          unknown                   None   \n",
       "...                  ...         ...        ...   \n",
       "DB15493              yes   inhibitor       None   \n",
       "DB15495              yes   inhibitor       None   \n",
       "DB15496              yes   inhibitor       None   \n",
       "DB15570          unknown  antagonist       None   \n",
       "DB15593              yes     inducer       None   \n",
       "\n",
       "                                                 name            type  \\\n",
       "drugbank_id                                                             \n",
       "DB00001                                     Lepirudin         biotech   \n",
       "DB00006                                   Bivalirudin  small molecule   \n",
       "DB00025      Antihemophilic factor, human recombinant         biotech   \n",
       "DB00055                              Drotrecogin alfa         biotech   \n",
       "DB00100           Coagulation Factor IX (Recombinant)         biotech   \n",
       "...                                               ...             ...   \n",
       "DB15493                                      Cambinol  small molecule   \n",
       "DB15495                                   Rocaglamide  small molecule   \n",
       "DB15496                        Didesmethylrocaglamide  small molecule   \n",
       "DB15570                                        FLX475  small molecule   \n",
       "DB15593                                    Golodirsen         biotech   \n",
       "\n",
       "                                         groups atc_codes  \\\n",
       "drugbank_id                                                 \n",
       "DB00001                                approved   B01AE02   \n",
       "DB00006                approved|investigational   B01AE06   \n",
       "DB00025                approved|investigational   B02BD02   \n",
       "DB00055      approved|investigational|withdrawn   B01AD10   \n",
       "DB00100                approved|investigational             \n",
       "...                                         ...       ...   \n",
       "DB15493                            experimental             \n",
       "DB15495                            experimental             \n",
       "DB15496                            experimental             \n",
       "DB15570                         investigational             \n",
       "DB15593                                approved             \n",
       "\n",
       "                                                    categories  \\\n",
       "drugbank_id                                                      \n",
       "DB00001      Amino Acids, Peptides, and Proteins|Anticoagul...   \n",
       "DB00006      Amino Acids, Peptides, and Proteins|Anticoagul...   \n",
       "DB00025      Amino Acids, Peptides, and Proteins|Biological...   \n",
       "DB00055      Amino Acids, Peptides, and Proteins|Anti-Infec...   \n",
       "DB00100      Blood Coagulation Factors|Hemostatics|Increase...   \n",
       "...                                                        ...   \n",
       "DB15493                                            Pyrimidines   \n",
       "DB15495                     Heterocyclic Compounds, Fused-Ring   \n",
       "DB15496                                                          \n",
       "DB15570                                                          \n",
       "DB15593      Drugs that are Mainly Renally Excreted|Oligonu...   \n",
       "\n",
       "                                                   description  \n",
       "drugbank_id                                                     \n",
       "DB00001      Lepirudin is identical to natural hirudin exce...  \n",
       "DB00006      Bivalirudin is a synthetic 20 residue peptide ...  \n",
       "DB00025      Human recombinant antihemophilic factor (AHF) ...  \n",
       "DB00055      Drotrecogin alfa is activated human protein C ...  \n",
       "DB00100      Recombinant Coagulation Factor IX is a purifie...  \n",
       "...                                                        ...  \n",
       "DB15493      Cambinol is a beta-naphtol derivative that inh...  \n",
       "DB15495      Rocaglamide, also referred to as rocaglamide-A...  \n",
       "DB15496      Didesmethylrocaglamide is a naturally-occurrin...  \n",
       "DB15570      FLX475 is a small molecule CCR4 antagonist bei...  \n",
       "DB15593      Golodirsen is a morpholino antisense oligomer ...  \n",
       "\n",
       "[27327 rows x 14 columns]"
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "entrez_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [],
   "source": [
    "entrez_df.index = np.arange(entrez_df.shape[0])\n",
    "results =  results.dropna().drop_duplicates().reset_index(drop=True)\n",
    "#entrez_df['hgnc_symbol'] = 0\n",
    "entrez_df['hgnc_symbol'] = entrez_df.entrez_gene_id.map(results['hgnc_symbol'])\n",
    "#for i in range(entrez_df.shape[0]):\n",
    "#    entrez_df.iloc[i,-1] = results.loc[results.entrezgene_id==entrez_df.iloc[i,3],'hgnc_symbol'][0].values#entrez_df.entrez_gene_id.map(results['hgnc_symbol'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(3005, 2)"
      ]
     },
     "execution_count": 29,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "results.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th>drugbank_id</th>\n",
       "      <th>category</th>\n",
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       "      <th>description</th>\n",
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       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>DB00001</td>\n",
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       "      <td>biotech</td>\n",
       "      <td>approved</td>\n",
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       "      <td>RET</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>DB00006</td>\n",
       "      <td>target</td>\n",
       "      <td>P00734</td>\n",
       "      <td>2147</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>inhibitor</td>\n",
       "      <td>None</td>\n",
       "      <td>Bivalirudin</td>\n",
       "      <td>small molecule</td>\n",
       "      <td>approved|investigational</td>\n",
       "      <td>B01AE06</td>\n",
       "      <td>Amino Acids, Peptides, and Proteins|Anticoagul...</td>\n",
       "      <td>Bivalirudin is a synthetic 20 residue peptide ...</td>\n",
       "      <td>RET</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>DB00025</td>\n",
       "      <td>enzyme</td>\n",
       "      <td>P00734</td>\n",
       "      <td>2147</td>\n",
       "      <td>Humans</td>\n",
       "      <td>unknown</td>\n",
       "      <td>activator</td>\n",
       "      <td>None</td>\n",
       "      <td>Antihemophilic factor, human recombinant</td>\n",
       "      <td>biotech</td>\n",
       "      <td>approved|investigational</td>\n",
       "      <td>B02BD02</td>\n",
       "      <td>Amino Acids, Peptides, and Proteins|Biological...</td>\n",
       "      <td>Human recombinant antihemophilic factor (AHF) ...</td>\n",
       "      <td>RET</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>DB00055</td>\n",
       "      <td>target</td>\n",
       "      <td>P00734</td>\n",
       "      <td>2147</td>\n",
       "      <td>Humans</td>\n",
       "      <td>unknown</td>\n",
       "      <td></td>\n",
       "      <td>None</td>\n",
       "      <td>Drotrecogin alfa</td>\n",
       "      <td>biotech</td>\n",
       "      <td>approved|investigational|withdrawn</td>\n",
       "      <td>B01AD10</td>\n",
       "      <td>Amino Acids, Peptides, and Proteins|Anti-Infec...</td>\n",
       "      <td>Drotrecogin alfa is activated human protein C ...</td>\n",
       "      <td>RET</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>DB00100</td>\n",
       "      <td>target</td>\n",
       "      <td>P00734</td>\n",
       "      <td>2147</td>\n",
       "      <td>Humans</td>\n",
       "      <td>unknown</td>\n",
       "      <td></td>\n",
       "      <td>None</td>\n",
       "      <td>Coagulation Factor IX (Recombinant)</td>\n",
       "      <td>biotech</td>\n",
       "      <td>approved|investigational</td>\n",
       "      <td></td>\n",
       "      <td>Blood Coagulation Factors|Hemostatics|Increase...</td>\n",
       "      <td>Recombinant Coagulation Factor IX is a purifie...</td>\n",
       "      <td>RET</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  drugbank_id category uniprot_id  entrez_gene_id organism known_action  \\\n",
       "0     DB00001   target     P00734            2147   Humans          yes   \n",
       "1     DB00006   target     P00734            2147   Humans          yes   \n",
       "2     DB00025   enzyme     P00734            2147   Humans      unknown   \n",
       "3     DB00055   target     P00734            2147   Humans      unknown   \n",
       "4     DB00100   target     P00734            2147   Humans      unknown   \n",
       "\n",
       "     actions pubmed_ids                                      name  \\\n",
       "0  inhibitor       None                                 Lepirudin   \n",
       "1  inhibitor       None                               Bivalirudin   \n",
       "2  activator       None  Antihemophilic factor, human recombinant   \n",
       "3                  None                          Drotrecogin alfa   \n",
       "4                  None       Coagulation Factor IX (Recombinant)   \n",
       "\n",
       "             type                              groups atc_codes  \\\n",
       "0         biotech                            approved   B01AE02   \n",
       "1  small molecule            approved|investigational   B01AE06   \n",
       "2         biotech            approved|investigational   B02BD02   \n",
       "3         biotech  approved|investigational|withdrawn   B01AD10   \n",
       "4         biotech            approved|investigational             \n",
       "\n",
       "                                          categories  \\\n",
       "0  Amino Acids, Peptides, and Proteins|Anticoagul...   \n",
       "1  Amino Acids, Peptides, and Proteins|Anticoagul...   \n",
       "2  Amino Acids, Peptides, and Proteins|Biological...   \n",
       "3  Amino Acids, Peptides, and Proteins|Anti-Infec...   \n",
       "4  Blood Coagulation Factors|Hemostatics|Increase...   \n",
       "\n",
       "                                         description hgnc_symbol  \n",
       "0  Lepirudin is identical to natural hirudin exce...         RET  \n",
       "1  Bivalirudin is a synthetic 20 residue peptide ...         RET  \n",
       "2  Human recombinant antihemophilic factor (AHF) ...         RET  \n",
       "3  Drotrecogin alfa is activated human protein C ...         RET  \n",
       "4  Recombinant Coagulation Factor IX is a purifie...         RET  "
      ]
     },
     "execution_count": 30,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "entrez_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [],
   "source": [
    "entrez_df.to_csv('DrugBank_Drug_Target.csv')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Integrate MedDRA side effect database"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 111,
   "metadata": {},
   "outputs": [],
   "source": [
    "se_df = pandas.read_csv('MedDRA/side-effects.tsv',sep='\\t') #pandas.read_csv('MedDRA/meddra_freq_with_cols.tsv',index_col=0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 112,
   "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>drugbank_id</th>\n",
       "      <th>drugbank_name</th>\n",
       "      <th>umls_cui_from_meddra</th>\n",
       "      <th>side_effect_name</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>DB07768</td>\n",
       "      <td>(10ALPHA,13ALPHA,14BETA,17ALPHA)-17-HYDROXYAND...</td>\n",
       "      <td>C0000729</td>\n",
       "      <td>Abdominal cramps</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>DB07768</td>\n",
       "      <td>(10ALPHA,13ALPHA,14BETA,17ALPHA)-17-HYDROXYAND...</td>\n",
       "      <td>C0000737</td>\n",
       "      <td>Abdominal pain</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>DB07768</td>\n",
       "      <td>(10ALPHA,13ALPHA,14BETA,17ALPHA)-17-HYDROXYAND...</td>\n",
       "      <td>C0232492</td>\n",
       "      <td>Abdominal pain upper</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>DB07768</td>\n",
       "      <td>(10ALPHA,13ALPHA,14BETA,17ALPHA)-17-HYDROXYAND...</td>\n",
       "      <td>C0740651</td>\n",
       "      <td>Abdominal symptom</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>DB07768</td>\n",
       "      <td>(10ALPHA,13ALPHA,14BETA,17ALPHA)-17-HYDROXYAND...</td>\n",
       "      <td>C0877331</td>\n",
       "      <td>Abnormal clotting factor</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  drugbank_id                                      drugbank_name  \\\n",
       "0     DB07768  (10ALPHA,13ALPHA,14BETA,17ALPHA)-17-HYDROXYAND...   \n",
       "1     DB07768  (10ALPHA,13ALPHA,14BETA,17ALPHA)-17-HYDROXYAND...   \n",
       "2     DB07768  (10ALPHA,13ALPHA,14BETA,17ALPHA)-17-HYDROXYAND...   \n",
       "3     DB07768  (10ALPHA,13ALPHA,14BETA,17ALPHA)-17-HYDROXYAND...   \n",
       "4     DB07768  (10ALPHA,13ALPHA,14BETA,17ALPHA)-17-HYDROXYAND...   \n",
       "\n",
       "  umls_cui_from_meddra          side_effect_name  \n",
       "0             C0000729          Abdominal cramps  \n",
       "1             C0000737            Abdominal pain  \n",
       "2             C0232492      Abdominal pain upper  \n",
       "3             C0740651         Abdominal symptom  \n",
       "4             C0877331  Abnormal clotting factor  "
      ]
     },
     "execution_count": 112,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "se_df.head(5)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 113,
   "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>umls_cui_from_meddra</th>\n",
       "      <th>side_effect_name</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>drugbank_id</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>DB00014</th>\n",
       "      <td>[C0000737, C0702166, C0948089, C0559546, C0233...</td>\n",
       "      <td>[Abdominal pain, Acne, Acute coronary syndrome...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB00035</th>\n",
       "      <td>[C1291077, C0000729, C0000731, C0000737, C0233...</td>\n",
       "      <td>[Abdominal bloating, Abdominal cramps, Abdomin...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                          umls_cui_from_meddra  \\\n",
       "drugbank_id                                                      \n",
       "DB00014      [C0000737, C0702166, C0948089, C0559546, C0233...   \n",
       "DB00035      [C1291077, C0000729, C0000731, C0000737, C0233...   \n",
       "\n",
       "                                              side_effect_name  \n",
       "drugbank_id                                                     \n",
       "DB00014      [Abdominal pain, Acne, Acute coronary syndrome...  \n",
       "DB00035      [Abdominal bloating, Abdominal cramps, Abdomin...  "
      ]
     },
     "execution_count": 113,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "se_df_unique = se_df.groupby('drugbank_id').agg({'umls_cui_from_meddra': lambda x: list(x),'umls_cui_from_meddra': lambda x: list(x),\n",
    "                                      'side_effect_name': lambda x: list(x),'side_effect_name': lambda x: list(x),\n",
    "                                     })\n",
    "se_df_unique.head(2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 114,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Maping side effect to drug bank using drukbank_id columns\n",
    "#se_df_unique.index = se_df_unique.drugbank_id\n",
    "#entrez_df.index = entrez_df.drugbank_id\n",
    "for i in ['umls_cui_from_meddra', 'side_effect_name']:\n",
    "    entrez_df[i] = entrez_df.drugbank_id.map(se_df_unique[i])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Integrate MedDRA indication database"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 64,
   "metadata": {
    "scrolled": true
   },
   "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>drugbank_id</th>\n",
       "      <th>drugbank_name</th>\n",
       "      <th>pubchem_id</th>\n",
       "      <th>stitch_id_flat</th>\n",
       "      <th>umls_cui_from_label</th>\n",
       "      <th>method</th>\n",
       "      <th>concept_name</th>\n",
       "      <th>meddra_type</th>\n",
       "      <th>umls_cui_from_meddra</th>\n",
       "      <th>meddra_name</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>DB00014</td>\n",
       "      <td>Goserelin</td>\n",
       "      <td>47725</td>\n",
       "      <td>CID100047725</td>\n",
       "      <td>C0002871</td>\n",
       "      <td>text_mention</td>\n",
       "      <td>Anemia</td>\n",
       "      <td>PT</td>\n",
       "      <td>C0002871</td>\n",
       "      <td>Anaemia</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>DB00014</td>\n",
       "      <td>Goserelin</td>\n",
       "      <td>47725</td>\n",
       "      <td>CID100047725</td>\n",
       "      <td>C0006142</td>\n",
       "      <td>NLP_indication</td>\n",
       "      <td>Malignant neoplasm of breast</td>\n",
       "      <td>PT</td>\n",
       "      <td>C0006142</td>\n",
       "      <td>Breast cancer</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>DB00014</td>\n",
       "      <td>Goserelin</td>\n",
       "      <td>47725</td>\n",
       "      <td>CID100047725</td>\n",
       "      <td>C0006826</td>\n",
       "      <td>NLP_precondition</td>\n",
       "      <td>Malignant Neoplasms</td>\n",
       "      <td>PT</td>\n",
       "      <td>C0006826</td>\n",
       "      <td>Neoplasm malignant</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>DB00014</td>\n",
       "      <td>Goserelin</td>\n",
       "      <td>47725</td>\n",
       "      <td>CID100047725</td>\n",
       "      <td>C0014175</td>\n",
       "      <td>NLP_indication</td>\n",
       "      <td>Endometriosis</td>\n",
       "      <td>PT</td>\n",
       "      <td>C0014175</td>\n",
       "      <td>Endometriosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>DB00014</td>\n",
       "      <td>Goserelin</td>\n",
       "      <td>47725</td>\n",
       "      <td>CID100047725</td>\n",
       "      <td>C0025323</td>\n",
       "      <td>text_mention</td>\n",
       "      <td>Menorrhagia</td>\n",
       "      <td>PT</td>\n",
       "      <td>C0025323</td>\n",
       "      <td>Menorrhagia</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  drugbank_id drugbank_name  pubchem_id stitch_id_flat umls_cui_from_label  \\\n",
       "0     DB00014     Goserelin       47725   CID100047725            C0002871   \n",
       "1     DB00014     Goserelin       47725   CID100047725            C0006142   \n",
       "2     DB00014     Goserelin       47725   CID100047725            C0006826   \n",
       "3     DB00014     Goserelin       47725   CID100047725            C0014175   \n",
       "4     DB00014     Goserelin       47725   CID100047725            C0025323   \n",
       "\n",
       "             method                  concept_name meddra_type  \\\n",
       "0      text_mention                        Anemia          PT   \n",
       "1    NLP_indication  Malignant neoplasm of breast          PT   \n",
       "2  NLP_precondition           Malignant Neoplasms          PT   \n",
       "3    NLP_indication                 Endometriosis          PT   \n",
       "4      text_mention                   Menorrhagia          PT   \n",
       "\n",
       "  umls_cui_from_meddra         meddra_name  \n",
       "0             C0002871             Anaemia  \n",
       "1             C0006142       Breast cancer  \n",
       "2             C0006826  Neoplasm malignant  \n",
       "3             C0014175       Endometriosis  \n",
       "4             C0025323         Menorrhagia  "
      ]
     },
     "execution_count": 64,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ind_df = pandas.read_csv('MedDRA/indications.tsv',sep='\\t')\n",
    "ind_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 65,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array(['text_mention', 'NLP_indication', 'NLP_precondition'], dtype=object)"
      ]
     },
     "execution_count": 65,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ind_df.method.unique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 97,
   "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>umls_cui_from_meddra</th>\n",
       "      <th>Meddra_Indication</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>drugbank_id</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>DB00014</th>\n",
       "      <td>[C0002871, C0006142, C0006826, C0014175, C0025...</td>\n",
       "      <td>[Anaemia, Bone cancer metastatic, Breast cance...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB00035</th>\n",
       "      <td>[C0008533, C0011848, C0032617, C0014394, C0018...</td>\n",
       "      <td>[Blood osmolarity decreased, Diabetes insipidu...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                          umls_cui_from_meddra  \\\n",
       "drugbank_id                                                      \n",
       "DB00014      [C0002871, C0006142, C0006826, C0014175, C0025...   \n",
       "DB00035      [C0008533, C0011848, C0032617, C0014394, C0018...   \n",
       "\n",
       "                                             Meddra_Indication  \n",
       "drugbank_id                                                     \n",
       "DB00014      [Anaemia, Bone cancer metastatic, Breast cance...  \n",
       "DB00035      [Blood osmolarity decreased, Diabetes insipidu...  "
      ]
     },
     "execution_count": 97,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ind_df_unique = ind_df.groupby('drugbank_id').agg({'umls_cui_from_meddra': lambda x: list(x),'umls_cui_from_meddra': lambda x: list(x),\n",
    "                                                   'meddra_name': lambda x: list(x),'meddra_name': lambda x: np.unique(list(x)).tolist(),\n",
    "                                                   })\n",
    "ind_df_unique.columns = ['umls_cui_from_meddra','Meddra_Indication']\n",
    "ind_df_unique.head(2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 98,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Maping indication to drug bank using drukbank_id columns\n",
    "#se_df_unique.index = se_df_unique.drugbank_id\n",
    "#entrez_df.index = entrez_df.drugbank_id\n",
    "for i in [ 'Meddra_Indication']:\n",
    "    entrez_df[i] = entrez_df.drugbank_id.map(ind_df_unique[i])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 99,
   "metadata": {},
   "outputs": [],
   "source": [
    "entrez_df.to_csv('DrugBank_Drug_Target_SideEffect_Indication.csv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 123,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\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>drugbank_id</th>\n",
       "      <th>drugbank_name</th>\n",
       "      <th>umls_cui_from_meddra</th>\n",
       "      <th>side_effect_name</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>DB07768</td>\n",
       "      <td>(10ALPHA,13ALPHA,14BETA,17ALPHA)-17-HYDROXYAND...</td>\n",
       "      <td>C0162820</td>\n",
       "      <td>Allergic contact dermatitis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>109</th>\n",
       "      <td>DB07768</td>\n",
       "      <td>(10ALPHA,13ALPHA,14BETA,17ALPHA)-17-HYDROXYAND...</td>\n",
       "      <td>C0011603</td>\n",
       "      <td>Dermatitis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>110</th>\n",
       "      <td>DB07768</td>\n",
       "      <td>(10ALPHA,13ALPHA,14BETA,17ALPHA)-17-HYDROXYAND...</td>\n",
       "      <td>C0234894</td>\n",
       "      <td>Dermatitis acneiform</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>111</th>\n",
       "      <td>DB07768</td>\n",
       "      <td>(10ALPHA,13ALPHA,14BETA,17ALPHA)-17-HYDROXYAND...</td>\n",
       "      <td>C0011615</td>\n",
       "      <td>Dermatitis atopic</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>112</th>\n",
       "      <td>DB07768</td>\n",
       "      <td>(10ALPHA,13ALPHA,14BETA,17ALPHA)-17-HYDROXYAND...</td>\n",
       "      <td>C0085932</td>\n",
       "      <td>Dermatitis bullous</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>153522</th>\n",
       "      <td>DB08439</td>\n",
       "      <td>parecoxib</td>\n",
       "      <td>C0019158</td>\n",
       "      <td>Hepatitis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>153549</th>\n",
       "      <td>DB08439</td>\n",
       "      <td>parecoxib</td>\n",
       "      <td>C0030305</td>\n",
       "      <td>Pancreatitis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>153576</th>\n",
       "      <td>DB05383</td>\n",
       "      <td>pimagedine HCl</td>\n",
       "      <td>C0011603</td>\n",
       "      <td>Dermatitis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>153605</th>\n",
       "      <td>DB07424</td>\n",
       "      <td>tripotassium (1R)-4-biphenyl-4-yl-1-phosphonat...</td>\n",
       "      <td>C0011603</td>\n",
       "      <td>Dermatitis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>153645</th>\n",
       "      <td>DB05738</td>\n",
       "      <td>vapitadine dihydrochloride</td>\n",
       "      <td>C0011603</td>\n",
       "      <td>Dermatitis</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>4053 rows × 4 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       drugbank_id                                      drugbank_name  \\\n",
       "15         DB07768  (10ALPHA,13ALPHA,14BETA,17ALPHA)-17-HYDROXYAND...   \n",
       "109        DB07768  (10ALPHA,13ALPHA,14BETA,17ALPHA)-17-HYDROXYAND...   \n",
       "110        DB07768  (10ALPHA,13ALPHA,14BETA,17ALPHA)-17-HYDROXYAND...   \n",
       "111        DB07768  (10ALPHA,13ALPHA,14BETA,17ALPHA)-17-HYDROXYAND...   \n",
       "112        DB07768  (10ALPHA,13ALPHA,14BETA,17ALPHA)-17-HYDROXYAND...   \n",
       "...            ...                                                ...   \n",
       "153522     DB08439                                          parecoxib   \n",
       "153549     DB08439                                          parecoxib   \n",
       "153576     DB05383                                     pimagedine HCl   \n",
       "153605     DB07424  tripotassium (1R)-4-biphenyl-4-yl-1-phosphonat...   \n",
       "153645     DB05738                         vapitadine dihydrochloride   \n",
       "\n",
       "       umls_cui_from_meddra             side_effect_name  \n",
       "15                 C0162820  Allergic contact dermatitis  \n",
       "109                C0011603                   Dermatitis  \n",
       "110                C0234894         Dermatitis acneiform  \n",
       "111                C0011615            Dermatitis atopic  \n",
       "112                C0085932           Dermatitis bullous  \n",
       "...                     ...                          ...  \n",
       "153522             C0019158                    Hepatitis  \n",
       "153549             C0030305                 Pancreatitis  \n",
       "153576             C0011603                   Dermatitis  \n",
       "153605             C0011603                   Dermatitis  \n",
       "153645             C0011603                   Dermatitis  \n",
       "\n",
       "[4053 rows x 4 columns]"
      ]
     },
     "execution_count": 123,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "idx = se_df.side_effect_name.str.lower().str.contains('titis')\n",
    "se_df_ = se_df.loc[idx,:]\n",
    "se_df_"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 100,
   "metadata": {},
   "outputs": [],
   "source": [
    "#entrez_df = entrez_df.drop(columns=['meddra_name'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 124,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(819, 4)"
      ]
     },
     "execution_count": 124,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "idx = np.logical_or(se_df.side_effect_name.str.lower().str.contains('toxic') , se_df.side_effect_name.str.contains('poisining'))\n",
    "se_df_ = se_df.loc[idx,:]\n",
    "se_df_.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 125,
   "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>drugbank_id</th>\n",
       "      <th>drugbank_name</th>\n",
       "      <th>umls_cui_from_meddra</th>\n",
       "      <th>side_effect_name</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>1214</th>\n",
       "      <td>DB08567</td>\n",
       "      <td>(1S,4S)-4-(3,4-dichlorophenyl)-N-methyl-1,2,3,...</td>\n",
       "      <td>C0014518</td>\n",
       "      <td>Toxic epidermal necrolysis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1329</th>\n",
       "      <td>DB07129</td>\n",
       "      <td>(2R)-1-(2,6-dimethylphenoxy)propan-2-amine</td>\n",
       "      <td>C0919924</td>\n",
       "      <td>Pulmonary toxicity</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1678</th>\n",
       "      <td>DB08298</td>\n",
       "      <td>(2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid</td>\n",
       "      <td>C0014518</td>\n",
       "      <td>Toxic epidermal necrolysis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1803</th>\n",
       "      <td>DB02932</td>\n",
       "      <td>(2r)-N-[4-Cyano-3-(Trifluoromethyl)Phenyl]-3-[...</td>\n",
       "      <td>C0235378</td>\n",
       "      <td>Hepatotoxicity</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2084</th>\n",
       "      <td>DB08472</td>\n",
       "      <td>(3R)-N-methyl-3-phenyl-3-[4-(trifluoromethyl)p...</td>\n",
       "      <td>C0876994</td>\n",
       "      <td>Cardiotoxicity</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>153072</th>\n",
       "      <td>DB05291</td>\n",
       "      <td>lidocaine patch</td>\n",
       "      <td>C3160947</td>\n",
       "      <td>CNS toxicity</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>153142</th>\n",
       "      <td>DB05291</td>\n",
       "      <td>lidocaine patch</td>\n",
       "      <td>C0235032</td>\n",
       "      <td>Neurotoxicity</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>153330</th>\n",
       "      <td>DB05302</td>\n",
       "      <td>naltrexone depot</td>\n",
       "      <td>C0235378</td>\n",
       "      <td>Hepatotoxicity</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>153565</th>\n",
       "      <td>DB08439</td>\n",
       "      <td>parecoxib</td>\n",
       "      <td>C0014518</td>\n",
       "      <td>Toxic epidermal necrolysis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>153625</th>\n",
       "      <td>DB07424</td>\n",
       "      <td>tripotassium (1R)-4-biphenyl-4-yl-1-phosphonat...</td>\n",
       "      <td>C0728899</td>\n",
       "      <td>Intoxication</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>819 rows × 4 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       drugbank_id                                      drugbank_name  \\\n",
       "1214       DB08567  (1S,4S)-4-(3,4-dichlorophenyl)-N-methyl-1,2,3,...   \n",
       "1329       DB07129         (2R)-1-(2,6-dimethylphenoxy)propan-2-amine   \n",
       "1678       DB08298    (2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid   \n",
       "1803       DB02932  (2r)-N-[4-Cyano-3-(Trifluoromethyl)Phenyl]-3-[...   \n",
       "2084       DB08472  (3R)-N-methyl-3-phenyl-3-[4-(trifluoromethyl)p...   \n",
       "...            ...                                                ...   \n",
       "153072     DB05291                                    lidocaine patch   \n",
       "153142     DB05291                                    lidocaine patch   \n",
       "153330     DB05302                                   naltrexone depot   \n",
       "153565     DB08439                                          parecoxib   \n",
       "153625     DB07424  tripotassium (1R)-4-biphenyl-4-yl-1-phosphonat...   \n",
       "\n",
       "       umls_cui_from_meddra            side_effect_name  \n",
       "1214               C0014518  Toxic epidermal necrolysis  \n",
       "1329               C0919924          Pulmonary toxicity  \n",
       "1678               C0014518  Toxic epidermal necrolysis  \n",
       "1803               C0235378              Hepatotoxicity  \n",
       "2084               C0876994              Cardiotoxicity  \n",
       "...                     ...                         ...  \n",
       "153072             C3160947                CNS toxicity  \n",
       "153142             C0235032               Neurotoxicity  \n",
       "153330             C0235378              Hepatotoxicity  \n",
       "153565             C0014518  Toxic epidermal necrolysis  \n",
       "153625             C0728899                Intoxication  \n",
       "\n",
       "[819 rows x 4 columns]"
      ]
     },
     "execution_count": 125,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "se_df_"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 103,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Selecting side effects with Toxicity only\n",
    "se_df_ = se_df.loc[idx,:]\n",
    "se_df_unique_ = se_df_.groupby('drugbank_id').agg({'umls_cui_from_meddra': lambda x: list(x),'umls_cui_from_meddra': lambda x: list(x),\n",
    "                                                 'side_effect_name': lambda x: list(x),'side_effect_name': lambda x: list(x),\n",
    "                                                 })\n",
    "for i in ['umls_cui_from_meddra', 'side_effect_name']:\n",
    "    entrez_df[i] = entrez_df.drugbank_id.map(se_df_unique_[i])\n",
    "entrez_df.to_csv('DrugBank_Drug_Target_Toxicity_Only_Indication.csv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 104,
   "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>drugbank_id</th>\n",
       "      <th>category</th>\n",
       "      <th>uniprot_id</th>\n",
       "      <th>entrez_gene_id</th>\n",
       "      <th>organism</th>\n",
       "      <th>known_action</th>\n",
       "      <th>actions</th>\n",
       "      <th>pubmed_ids</th>\n",
       "      <th>name</th>\n",
       "      <th>type</th>\n",
       "      <th>groups</th>\n",
       "      <th>atc_codes</th>\n",
       "      <th>categories</th>\n",
       "      <th>description</th>\n",
       "      <th>hgnc_symbol</th>\n",
       "      <th>umls_cui_from_meddra</th>\n",
       "      <th>side_effect_name</th>\n",
       "      <th>Meddra_Indication</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>DB00001</td>\n",
       "      <td>target</td>\n",
       "      <td>P00734</td>\n",
       "      <td>2147</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>inhibitor</td>\n",
       "      <td>None</td>\n",
       "      <td>Lepirudin</td>\n",
       "      <td>biotech</td>\n",
       "      <td>approved</td>\n",
       "      <td>B01AE02</td>\n",
       "      <td>Amino Acids, Peptides, and Proteins|Anticoagul...</td>\n",
       "      <td>Lepirudin is identical to natural hirudin exce...</td>\n",
       "      <td>RET</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>DB00006</td>\n",
       "      <td>target</td>\n",
       "      <td>P00734</td>\n",
       "      <td>2147</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>inhibitor</td>\n",
       "      <td>None</td>\n",
       "      <td>Bivalirudin</td>\n",
       "      <td>small molecule</td>\n",
       "      <td>approved|investigational</td>\n",
       "      <td>B01AE06</td>\n",
       "      <td>Amino Acids, Peptides, and Proteins|Anticoagul...</td>\n",
       "      <td>Bivalirudin is a synthetic 20 residue peptide ...</td>\n",
       "      <td>RET</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>DB00025</td>\n",
       "      <td>enzyme</td>\n",
       "      <td>P00734</td>\n",
       "      <td>2147</td>\n",
       "      <td>Humans</td>\n",
       "      <td>unknown</td>\n",
       "      <td>activator</td>\n",
       "      <td>None</td>\n",
       "      <td>Antihemophilic factor, human recombinant</td>\n",
       "      <td>biotech</td>\n",
       "      <td>approved|investigational</td>\n",
       "      <td>B02BD02</td>\n",
       "      <td>Amino Acids, Peptides, and Proteins|Biological...</td>\n",
       "      <td>Human recombinant antihemophilic factor (AHF) ...</td>\n",
       "      <td>RET</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>DB00055</td>\n",
       "      <td>target</td>\n",
       "      <td>P00734</td>\n",
       "      <td>2147</td>\n",
       "      <td>Humans</td>\n",
       "      <td>unknown</td>\n",
       "      <td></td>\n",
       "      <td>None</td>\n",
       "      <td>Drotrecogin alfa</td>\n",
       "      <td>biotech</td>\n",
       "      <td>approved|investigational|withdrawn</td>\n",
       "      <td>B01AD10</td>\n",
       "      <td>Amino Acids, Peptides, and Proteins|Anti-Infec...</td>\n",
       "      <td>Drotrecogin alfa is activated human protein C ...</td>\n",
       "      <td>RET</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>DB00100</td>\n",
       "      <td>target</td>\n",
       "      <td>P00734</td>\n",
       "      <td>2147</td>\n",
       "      <td>Humans</td>\n",
       "      <td>unknown</td>\n",
       "      <td></td>\n",
       "      <td>None</td>\n",
       "      <td>Coagulation Factor IX (Recombinant)</td>\n",
       "      <td>biotech</td>\n",
       "      <td>approved|investigational</td>\n",
       "      <td></td>\n",
       "      <td>Blood Coagulation Factors|Hemostatics|Increase...</td>\n",
       "      <td>Recombinant Coagulation Factor IX is a purifie...</td>\n",
       "      <td>RET</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  drugbank_id category uniprot_id  entrez_gene_id organism known_action  \\\n",
       "0     DB00001   target     P00734            2147   Humans          yes   \n",
       "1     DB00006   target     P00734            2147   Humans          yes   \n",
       "2     DB00025   enzyme     P00734            2147   Humans      unknown   \n",
       "3     DB00055   target     P00734            2147   Humans      unknown   \n",
       "4     DB00100   target     P00734            2147   Humans      unknown   \n",
       "\n",
       "     actions pubmed_ids                                      name  \\\n",
       "0  inhibitor       None                                 Lepirudin   \n",
       "1  inhibitor       None                               Bivalirudin   \n",
       "2  activator       None  Antihemophilic factor, human recombinant   \n",
       "3                  None                          Drotrecogin alfa   \n",
       "4                  None       Coagulation Factor IX (Recombinant)   \n",
       "\n",
       "             type                              groups atc_codes  \\\n",
       "0         biotech                            approved   B01AE02   \n",
       "1  small molecule            approved|investigational   B01AE06   \n",
       "2         biotech            approved|investigational   B02BD02   \n",
       "3         biotech  approved|investigational|withdrawn   B01AD10   \n",
       "4         biotech            approved|investigational             \n",
       "\n",
       "                                          categories  \\\n",
       "0  Amino Acids, Peptides, and Proteins|Anticoagul...   \n",
       "1  Amino Acids, Peptides, and Proteins|Anticoagul...   \n",
       "2  Amino Acids, Peptides, and Proteins|Biological...   \n",
       "3  Amino Acids, Peptides, and Proteins|Anti-Infec...   \n",
       "4  Blood Coagulation Factors|Hemostatics|Increase...   \n",
       "\n",
       "                                         description hgnc_symbol  \\\n",
       "0  Lepirudin is identical to natural hirudin exce...         RET   \n",
       "1  Bivalirudin is a synthetic 20 residue peptide ...         RET   \n",
       "2  Human recombinant antihemophilic factor (AHF) ...         RET   \n",
       "3  Drotrecogin alfa is activated human protein C ...         RET   \n",
       "4  Recombinant Coagulation Factor IX is a purifie...         RET   \n",
       "\n",
       "  umls_cui_from_meddra side_effect_name Meddra_Indication  \n",
       "0                  NaN              NaN               NaN  \n",
       "1                  NaN              NaN               NaN  \n",
       "2                  NaN              NaN               NaN  \n",
       "3                  NaN              NaN               NaN  \n",
       "4                  NaN              NaN               NaN  "
      ]
     },
     "execution_count": 104,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "entrez_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 105,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Drugbank entries with SE only\n",
    "entrez_df_with_se = entrez_df.loc[~entrez_df.side_effect_name.isna(),:]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 106,
   "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>drugbank_id</th>\n",
       "      <th>category</th>\n",
       "      <th>uniprot_id</th>\n",
       "      <th>entrez_gene_id</th>\n",
       "      <th>organism</th>\n",
       "      <th>known_action</th>\n",
       "      <th>actions</th>\n",
       "      <th>pubmed_ids</th>\n",
       "      <th>name</th>\n",
       "      <th>type</th>\n",
       "      <th>groups</th>\n",
       "      <th>atc_codes</th>\n",
       "      <th>categories</th>\n",
       "      <th>description</th>\n",
       "      <th>hgnc_symbol</th>\n",
       "      <th>umls_cui_from_meddra</th>\n",
       "      <th>side_effect_name</th>\n",
       "      <th>Meddra_Indication</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>121</th>\n",
       "      <td>DB00281</td>\n",
       "      <td>target</td>\n",
       "      <td>P00533</td>\n",
       "      <td>1956</td>\n",
       "      <td>Humans</td>\n",
       "      <td>unknown</td>\n",
       "      <td>antagonist</td>\n",
       "      <td>None</td>\n",
       "      <td>Lidocaine</td>\n",
       "      <td>small molecule</td>\n",
       "      <td>approved|vet_approved</td>\n",
       "      <td>S01HA07|D04AB01|R02AD02|C01BB01|S02DA01|N01BB5...</td>\n",
       "      <td>Agents for Treatment of Hemorrhoids and Anal F...</td>\n",
       "      <td>Ever since its discovery and availability for ...</td>\n",
       "      <td>ACOT13</td>\n",
       "      <td>[C3160947, C0235032]</td>\n",
       "      <td>[CNS toxicity, Neurotoxicity]</td>\n",
       "      <td>[Acute coronary syndrome, Acute myocardial inf...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>122</th>\n",
       "      <td>DB00317</td>\n",
       "      <td>target</td>\n",
       "      <td>P00533</td>\n",
       "      <td>1956</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>antagonist</td>\n",
       "      <td>None</td>\n",
       "      <td>Gefitinib</td>\n",
       "      <td>small molecule</td>\n",
       "      <td>approved|investigational</td>\n",
       "      <td>L01XE02</td>\n",
       "      <td>Antineoplastic Agents|Antineoplastic and Immun...</td>\n",
       "      <td>Gefitinib (originally coded ZD1839) is a drug ...</td>\n",
       "      <td>ACOT13</td>\n",
       "      <td>[C0919924]</td>\n",
       "      <td>[Pulmonary toxicity]</td>\n",
       "      <td>[Haemoglobin, Haemorrhage, Idiopathic pulmonar...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>123</th>\n",
       "      <td>DB00530</td>\n",
       "      <td>target</td>\n",
       "      <td>P00533</td>\n",
       "      <td>1956</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>antagonist</td>\n",
       "      <td>None</td>\n",
       "      <td>Erlotinib</td>\n",
       "      <td>small molecule</td>\n",
       "      <td>approved|investigational</td>\n",
       "      <td>L01XE03</td>\n",
       "      <td>Antineoplastic Agents|Antineoplastic and Immun...</td>\n",
       "      <td>Erlotinib is an inhibitor of the epidermal gro...</td>\n",
       "      <td>ACOT13</td>\n",
       "      <td>[C0235378, C0919924]</td>\n",
       "      <td>[Hepatotoxicity, Pulmonary toxicity]</td>\n",
       "      <td>[Metastases to pancreas, Neoplasm, Neoplasm ma...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>124</th>\n",
       "      <td>DB01259</td>\n",
       "      <td>target</td>\n",
       "      <td>P00533</td>\n",
       "      <td>1956</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>antagonist</td>\n",
       "      <td>None</td>\n",
       "      <td>Lapatinib</td>\n",
       "      <td>small molecule</td>\n",
       "      <td>approved|investigational</td>\n",
       "      <td>L01XE07</td>\n",
       "      <td>Antineoplastic Agents|Antineoplastic and Immun...</td>\n",
       "      <td>Lapatinib is an anti-cancer drug developed by ...</td>\n",
       "      <td>ACOT13</td>\n",
       "      <td>[C0876994, C0235378]</td>\n",
       "      <td>[Cardiotoxicity, Hepatotoxicity]</td>\n",
       "      <td>[Breast cancer, Breast cancer stage IV, Diseas...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>137</th>\n",
       "      <td>DB08916</td>\n",
       "      <td>target</td>\n",
       "      <td>P00533</td>\n",
       "      <td>1956</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>inhibitor</td>\n",
       "      <td>None</td>\n",
       "      <td>Afatinib</td>\n",
       "      <td>small molecule</td>\n",
       "      <td>approved</td>\n",
       "      <td>L01XE13</td>\n",
       "      <td>Amides|Antineoplastic Agents|Antineoplastic an...</td>\n",
       "      <td>Afatinib is a 4-anilinoquinazoline tyrosine ki...</td>\n",
       "      <td>ACOT13</td>\n",
       "      <td>[C0919924]</td>\n",
       "      <td>[Pulmonary toxicity]</td>\n",
       "      <td>[Neoplasm, Non-small cell lung cancer, Small c...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    drugbank_id category uniprot_id  entrez_gene_id organism known_action  \\\n",
       "121     DB00281   target     P00533            1956   Humans      unknown   \n",
       "122     DB00317   target     P00533            1956   Humans          yes   \n",
       "123     DB00530   target     P00533            1956   Humans          yes   \n",
       "124     DB01259   target     P00533            1956   Humans          yes   \n",
       "137     DB08916   target     P00533            1956   Humans          yes   \n",
       "\n",
       "        actions pubmed_ids       name            type  \\\n",
       "121  antagonist       None  Lidocaine  small molecule   \n",
       "122  antagonist       None  Gefitinib  small molecule   \n",
       "123  antagonist       None  Erlotinib  small molecule   \n",
       "124  antagonist       None  Lapatinib  small molecule   \n",
       "137   inhibitor       None   Afatinib  small molecule   \n",
       "\n",
       "                       groups  \\\n",
       "121     approved|vet_approved   \n",
       "122  approved|investigational   \n",
       "123  approved|investigational   \n",
       "124  approved|investigational   \n",
       "137                  approved   \n",
       "\n",
       "                                             atc_codes  \\\n",
       "121  S01HA07|D04AB01|R02AD02|C01BB01|S02DA01|N01BB5...   \n",
       "122                                            L01XE02   \n",
       "123                                            L01XE03   \n",
       "124                                            L01XE07   \n",
       "137                                            L01XE13   \n",
       "\n",
       "                                            categories  \\\n",
       "121  Agents for Treatment of Hemorrhoids and Anal F...   \n",
       "122  Antineoplastic Agents|Antineoplastic and Immun...   \n",
       "123  Antineoplastic Agents|Antineoplastic and Immun...   \n",
       "124  Antineoplastic Agents|Antineoplastic and Immun...   \n",
       "137  Amides|Antineoplastic Agents|Antineoplastic an...   \n",
       "\n",
       "                                           description hgnc_symbol  \\\n",
       "121  Ever since its discovery and availability for ...      ACOT13   \n",
       "122  Gefitinib (originally coded ZD1839) is a drug ...      ACOT13   \n",
       "123  Erlotinib is an inhibitor of the epidermal gro...      ACOT13   \n",
       "124  Lapatinib is an anti-cancer drug developed by ...      ACOT13   \n",
       "137  Afatinib is a 4-anilinoquinazoline tyrosine ki...      ACOT13   \n",
       "\n",
       "     umls_cui_from_meddra                      side_effect_name  \\\n",
       "121  [C3160947, C0235032]         [CNS toxicity, Neurotoxicity]   \n",
       "122            [C0919924]                  [Pulmonary toxicity]   \n",
       "123  [C0235378, C0919924]  [Hepatotoxicity, Pulmonary toxicity]   \n",
       "124  [C0876994, C0235378]      [Cardiotoxicity, Hepatotoxicity]   \n",
       "137            [C0919924]                  [Pulmonary toxicity]   \n",
       "\n",
       "                                     Meddra_Indication  \n",
       "121  [Acute coronary syndrome, Acute myocardial inf...  \n",
       "122  [Haemoglobin, Haemorrhage, Idiopathic pulmonar...  \n",
       "123  [Metastases to pancreas, Neoplasm, Neoplasm ma...  \n",
       "124  [Breast cancer, Breast cancer stage IV, Diseas...  \n",
       "137  [Neoplasm, Non-small cell lung cancer, Small c...  "
      ]
     },
     "execution_count": 106,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "entrez_df_with_se.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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