2021-08-11-drugbank/2021-08-11-drugbank.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "threaded-retail",
   "metadata": {},
   "source": [
    "Downloading and parsing drugbank"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "married-classroom",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "GenRev not found, steiner wont work\n",
      "Import error: Negex. Using keyword matching instead\n",
      "Import error: Funcassociate. Make sure that funcassociate is in toolbox!\n"
     ]
    }
   ],
   "source": [
    "%load_ext autoreload\n",
    "%autoreload 2\n",
    "%reload_ext autoreload\n",
    "#from drugbank_downloader import download_drugbank, open_drugbank\n",
    "import repos_tools\n",
    "import xml.etree.ElementTree as ET\n",
    "import pandas as pd\n",
    "import re\n",
    "import matplotlib.pyplot as plt\n",
    "import attila_utils"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "balanced-reservation",
   "metadata": {},
   "source": [
    "The `download_drugbank` function of `drugbank_downloader` failed with `TypeError: get_config() takes 2 positional arguments but 3 were given`."
   ]
  },
  {
   "cell_type": "raw",
   "id": "moving-louisville",
   "metadata": {},
   "source": [
    "username = os.getenv('DRUGBANK_USERNAME')\n",
    "password = os.getenv('DRUGBANK_PASSWORD')\n",
    "path = download_drugbank(version='5.1.8', username=username, password=password)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "given-metropolitan",
   "metadata": {},
   "source": [
    "Fortunately, another drugbank parser, written by [dhimmel](https://github.com/dhimmel), worked seamlessly; see below.\n",
    "\n",
    "## dhimmel's parser\n",
    "\n",
    "I took dhimmel's code from [parse.ipynb](https://github.com/dhimmel/drugbank/blob/gh-pages/parse.ipynb) and wrapped two code blocks in two functions of the `repos_tools` module:\n",
    "1. `get_drugbank_drugs`\n",
    "1. `get_drugbank_proteins`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "radical-hands",
   "metadata": {},
   "outputs": [],
   "source": [
    "root = repos_tools.get_drugbank_xml_root(xml_path='../../resources/drugbank/drugbank.5.1.8.xml')"
   ]
  },
  {
   "cell_type": "raw",
   "id": "experienced-theorem",
   "metadata": {},
   "source": [
    "xml_path = '../../resources/drugbank/drugbank.5.1.8.xml'\n",
    "with open(xml_path) as xml_file:\n",
    "    tree = ET.parse(xml_file)\n",
    "root = tree.getroot()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "serial-persian",
   "metadata": {},
   "source": [
    "Getting drugs in a DataFrame."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "material-reservation",
   "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",
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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>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",
       "    <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",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>DB00001</th>\n",
       "      <td>Lepirudin</td>\n",
       "      <td>biotech</td>\n",
       "      <td>approved</td>\n",
       "      <td>[B01AE02]</td>\n",
       "      <td>[Amino Acids, Peptides, and Proteins, Anticoag...</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>DB00002</th>\n",
       "      <td>Cetuximab</td>\n",
       "      <td>biotech</td>\n",
       "      <td>approved</td>\n",
       "      <td>[L01XC06]</td>\n",
       "      <td>[Amino Acids, Peptides, and Proteins, Antibodi...</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>DB00003</th>\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 an...</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>DB00004</th>\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, Peptide...</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>DB00005</th>\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,...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>Dimeric fusion protein consisting of the extra...</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>DB16420</th>\n",
       "      <td>Vibostolimab</td>\n",
       "      <td>biotech</td>\n",
       "      <td>investigational</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>Vibostolimab is under investigation in clinica...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB16421</th>\n",
       "      <td>Volagidemab</td>\n",
       "      <td>biotech</td>\n",
       "      <td>investigational</td>\n",
       "      <td>[]</td>\n",
       "      <td>[Amino Acids, Peptides, and Proteins, Antibodi...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>Volagidemab is under investigation in clinical...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB16422</th>\n",
       "      <td>Quavonlimab</td>\n",
       "      <td>biotech</td>\n",
       "      <td>investigational</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>Quavonlimab is under investigation in clinical...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB16423</th>\n",
       "      <td>AK119</td>\n",
       "      <td>biotech</td>\n",
       "      <td>investigational</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>AK119 is a humanized anti-CD73 monoclonal anti...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB16424</th>\n",
       "      <td>Allocetra</td>\n",
       "      <td>biotech</td>\n",
       "      <td>investigational</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>Allocetra is a novel therapy where billions of...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>14315 rows × 8 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                            name     type                    groups  \\\n",
       "drugbank_id                                                           \n",
       "DB00001                Lepirudin  biotech                  approved   \n",
       "DB00002                Cetuximab  biotech                  approved   \n",
       "DB00003             Dornase alfa  biotech                  approved   \n",
       "DB00004      Denileukin diftitox  biotech  approved|investigational   \n",
       "DB00005               Etanercept  biotech  approved|investigational   \n",
       "...                          ...      ...                       ...   \n",
       "DB16420             Vibostolimab  biotech           investigational   \n",
       "DB16421              Volagidemab  biotech           investigational   \n",
       "DB16422              Quavonlimab  biotech           investigational   \n",
       "DB16423                    AK119  biotech           investigational   \n",
       "DB16424                Allocetra  biotech           investigational   \n",
       "\n",
       "             atc_codes                                         categories  \\\n",
       "drugbank_id                                                                 \n",
       "DB00001      [B01AE02]  [Amino Acids, Peptides, and Proteins, Anticoag...   \n",
       "DB00002      [L01XC06]  [Amino Acids, Peptides, and Proteins, Antibodi...   \n",
       "DB00003      [R05CB13]  [Amino Acids, Peptides, and Proteins, Cough an...   \n",
       "DB00004      [L01XX29]  [ADP Ribose Transferases, Amino Acids, Peptide...   \n",
       "DB00005      [L04AB01]  [Agents reducing cytokine levels, Amino Acids,...   \n",
       "...                ...                                                ...   \n",
       "DB16420             []                                                 []   \n",
       "DB16421             []  [Amino Acids, Peptides, and Proteins, Antibodi...   \n",
       "DB16422             []                                                 []   \n",
       "DB16423             []                                                 []   \n",
       "DB16424             []                                                 []   \n",
       "\n",
       "            inchikey inchi                                        description  \n",
       "drugbank_id                                                                    \n",
       "DB00001         None  None  Lepirudin is identical to natural hirudin exce...  \n",
       "DB00002         None  None  Cetuximab is an epidermal growth factor recept...  \n",
       "DB00003         None  None  Dornase alfa is a biosynthetic form of human d...  \n",
       "DB00004         None  None  A recombinant DNA-derived cytotoxic protein co...  \n",
       "DB00005         None  None  Dimeric fusion protein consisting of the extra...  \n",
       "...              ...   ...                                                ...  \n",
       "DB16420         None  None  Vibostolimab is under investigation in clinica...  \n",
       "DB16421         None  None  Volagidemab is under investigation in clinical...  \n",
       "DB16422         None  None  Quavonlimab is under investigation in clinical...  \n",
       "DB16423         None  None  AK119 is a humanized anti-CD73 monoclonal anti...  \n",
       "DB16424         None  None  Allocetra is a novel therapy where billions of...  \n",
       "\n",
       "[14315 rows x 8 columns]"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "drugs = repos_tools.get_drugbank_drugs(root)\n",
    "drugs.to_csv('../../results/2021-08-11-drugbank/drugbank-all-drugs.csv')\n",
    "drugs"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "present-domain",
   "metadata": {},
   "source": [
    "Getting proteins into a DataFrame.  The HGNC ID will be used to obtain the corresponding NCBI Entrez GeneID."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "peripheral-electricity",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th>category</th>\n",
       "      <th>organism</th>\n",
       "      <th>known_action</th>\n",
       "      <th>actions</th>\n",
       "      <th>name</th>\n",
       "      <th>hgnc_id</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>drugbank_id</th>\n",
       "      <th>uniprot_id</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",
       "      <th>P00734</th>\n",
       "      <td>target</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>inhibitor</td>\n",
       "      <td>Prothrombin</td>\n",
       "      <td>HGNC:3535</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th rowspan=\"4\" valign=\"top\">DB00002</th>\n",
       "      <th>P00533</th>\n",
       "      <td>target</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>antagonist</td>\n",
       "      <td>Epidermal growth factor receptor</td>\n",
       "      <td>HGNC:3236</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>O75015</th>\n",
       "      <td>target</td>\n",
       "      <td>Humans</td>\n",
       "      <td>unknown</td>\n",
       "      <td></td>\n",
       "      <td>Low affinity immunoglobulin gamma Fc region re...</td>\n",
       "      <td>HGNC:3620</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>P02745</th>\n",
       "      <td>target</td>\n",
       "      <td>Humans</td>\n",
       "      <td>unknown</td>\n",
       "      <td></td>\n",
       "      <td>Complement C1q subcomponent subunit A</td>\n",
       "      <td>HGNC:1241</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>P02746</th>\n",
       "      <td>target</td>\n",
       "      <td>Humans</td>\n",
       "      <td>unknown</td>\n",
       "      <td></td>\n",
       "      <td>Complement C1q subcomponent subunit B</td>\n",
       "      <td>HGNC:1242</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB15982</th>\n",
       "      <th>Q9UNQ0</th>\n",
       "      <td>transporter</td>\n",
       "      <td>Humans</td>\n",
       "      <td>unknown</td>\n",
       "      <td>substrate</td>\n",
       "      <td>ATP-binding cassette sub-family G member 2</td>\n",
       "      <td>HGNC:74</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB16019</th>\n",
       "      <th>P07288</th>\n",
       "      <td>target</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>binder</td>\n",
       "      <td>Prostate-specific antigen</td>\n",
       "      <td>HGNC:6364</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB16353</th>\n",
       "      <th>P23467</th>\n",
       "      <td>target</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>inhibitor</td>\n",
       "      <td>Receptor-type tyrosine-protein phosphatase beta</td>\n",
       "      <td>HGNC:9665</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB16370</th>\n",
       "      <th>P28907</th>\n",
       "      <td>target</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>inhibitor</td>\n",
       "      <td>ADP-ribosyl cyclase 1</td>\n",
       "      <td>HGNC:1667</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB16385</th>\n",
       "      <th>Q05320</th>\n",
       "      <td>target</td>\n",
       "      <td>Zaire ebolavirus (strain Mayinga-76)</td>\n",
       "      <td>yes</td>\n",
       "      <td>antagonist</td>\n",
       "      <td>Envelope glycoprotein</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>27169 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                           category                              organism  \\\n",
       "drugbank_id uniprot_id                                                      \n",
       "DB00001     P00734           target                                Humans   \n",
       "DB00002     P00533           target                                Humans   \n",
       "            O75015           target                                Humans   \n",
       "            P02745           target                                Humans   \n",
       "            P02746           target                                Humans   \n",
       "...                             ...                                   ...   \n",
       "DB15982     Q9UNQ0      transporter                                Humans   \n",
       "DB16019     P07288           target                                Humans   \n",
       "DB16353     P23467           target                                Humans   \n",
       "DB16370     P28907           target                                Humans   \n",
       "DB16385     Q05320           target  Zaire ebolavirus (strain Mayinga-76)   \n",
       "\n",
       "                       known_action     actions  \\\n",
       "drugbank_id uniprot_id                            \n",
       "DB00001     P00734              yes   inhibitor   \n",
       "DB00002     P00533              yes  antagonist   \n",
       "            O75015          unknown               \n",
       "            P02745          unknown               \n",
       "            P02746          unknown               \n",
       "...                             ...         ...   \n",
       "DB15982     Q9UNQ0          unknown   substrate   \n",
       "DB16019     P07288              yes      binder   \n",
       "DB16353     P23467              yes   inhibitor   \n",
       "DB16370     P28907              yes   inhibitor   \n",
       "DB16385     Q05320              yes  antagonist   \n",
       "\n",
       "                                                                     name  \\\n",
       "drugbank_id uniprot_id                                                      \n",
       "DB00001     P00734                                            Prothrombin   \n",
       "DB00002     P00533                       Epidermal growth factor receptor   \n",
       "            O75015      Low affinity immunoglobulin gamma Fc region re...   \n",
       "            P02745                  Complement C1q subcomponent subunit A   \n",
       "            P02746                  Complement C1q subcomponent subunit B   \n",
       "...                                                                   ...   \n",
       "DB15982     Q9UNQ0             ATP-binding cassette sub-family G member 2   \n",
       "DB16019     P07288                              Prostate-specific antigen   \n",
       "DB16353     P23467        Receptor-type tyrosine-protein phosphatase beta   \n",
       "DB16370     P28907                                  ADP-ribosyl cyclase 1   \n",
       "DB16385     Q05320                                  Envelope glycoprotein   \n",
       "\n",
       "                          hgnc_id  \n",
       "drugbank_id uniprot_id             \n",
       "DB00001     P00734      HGNC:3535  \n",
       "DB00002     P00533      HGNC:3236  \n",
       "            O75015      HGNC:3620  \n",
       "            P02745      HGNC:1241  \n",
       "            P02746      HGNC:1242  \n",
       "...                           ...  \n",
       "DB15982     Q9UNQ0        HGNC:74  \n",
       "DB16019     P07288      HGNC:6364  \n",
       "DB16353     P23467      HGNC:9665  \n",
       "DB16370     P28907      HGNC:1667  \n",
       "DB16385     Q05320            NaN  \n",
       "\n",
       "[27169 rows x 6 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "proteins = repos_tools.get_drugbank_proteins(root)\n",
    "proteins.to_csv('../../results/2021-08-11-drugbank/drugbank-all-proteins.csv')\n",
    "proteins"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "abroad-quilt",
   "metadata": {},
   "source": [
    "## Filtering and cleaning\n",
    "\n",
    "Keep only those proteins that fulfill all below (see `filter_drugbank_proteins` function):\n",
    "* are human proteins \n",
    "* are targets of small molecules \n",
    "* possess a HGNC ID\n",
    "\n",
    "Also, extend filtered protein_df with symbol, entrez id, and group (see `extend_with_entrez_id` function)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "shared-probe",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th>symbol</th>\n",
       "      <th>name</th>\n",
       "      <th>category</th>\n",
       "      <th>organism</th>\n",
       "      <th>known_action</th>\n",
       "      <th>actions</th>\n",
       "      <th>hgnc_id</th>\n",
       "      <th>group</th>\n",
       "      <th>entrez_id</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>drugbank_id</th>\n",
       "      <th>uniprot_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",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>DB00006</th>\n",
       "      <th>P00734</th>\n",
       "      <td>F2</td>\n",
       "      <td>Prothrombin</td>\n",
       "      <td>target</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>inhibitor</td>\n",
       "      <td>HGNC:3535</td>\n",
       "      <td>approved</td>\n",
       "      <td>2147</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB00007</th>\n",
       "      <th>P30968</th>\n",
       "      <td>GNRHR</td>\n",
       "      <td>Gonadotropin-releasing hormone receptor</td>\n",
       "      <td>target</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>agonist</td>\n",
       "      <td>HGNC:4421</td>\n",
       "      <td>approved</td>\n",
       "      <td>2798</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th rowspan=\"2\" valign=\"top\">DB00014</th>\n",
       "      <th>P22888</th>\n",
       "      <td>LHCGR</td>\n",
       "      <td>Lutropin-choriogonadotropic hormone receptor</td>\n",
       "      <td>target</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>agonist</td>\n",
       "      <td>HGNC:6585</td>\n",
       "      <td>approved</td>\n",
       "      <td>3973</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>P30968</th>\n",
       "      <td>GNRHR</td>\n",
       "      <td>Gonadotropin-releasing hormone receptor</td>\n",
       "      <td>target</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>agonist</td>\n",
       "      <td>HGNC:4421</td>\n",
       "      <td>approved</td>\n",
       "      <td>2798</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB00035</th>\n",
       "      <th>P30518</th>\n",
       "      <td>AVPR2</td>\n",
       "      <td>Vasopressin V2 receptor</td>\n",
       "      <td>target</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>agonist</td>\n",
       "      <td>HGNC:897</td>\n",
       "      <td>approved</td>\n",
       "      <td>554</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB15822</th>\n",
       "      <th>P21802</th>\n",
       "      <td>FGFR2</td>\n",
       "      <td>Fibroblast growth factor receptor 2</td>\n",
       "      <td>target</td>\n",
       "      <td>Humans</td>\n",
       "      <td>unknown</td>\n",
       "      <td>inhibitor</td>\n",
       "      <td>HGNC:3689</td>\n",
       "      <td>approved</td>\n",
       "      <td>2263</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB15873</th>\n",
       "      <th>P30874</th>\n",
       "      <td>SSTR2</td>\n",
       "      <td>Somatostatin receptor type 2</td>\n",
       "      <td>target</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>binder</td>\n",
       "      <td>HGNC:11331</td>\n",
       "      <td>approved</td>\n",
       "      <td>6752</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB15982</th>\n",
       "      <th>P03952</th>\n",
       "      <td>KLKB1</td>\n",
       "      <td>Plasma kallikrein</td>\n",
       "      <td>target</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>inhibitor</td>\n",
       "      <td>HGNC:6371</td>\n",
       "      <td>approved</td>\n",
       "      <td>3818</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB16019</th>\n",
       "      <th>P07288</th>\n",
       "      <td>KLK3</td>\n",
       "      <td>Prostate-specific antigen</td>\n",
       "      <td>target</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>binder</td>\n",
       "      <td>HGNC:6364</td>\n",
       "      <td>approved</td>\n",
       "      <td>354</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB16353</th>\n",
       "      <th>P23467</th>\n",
       "      <td>PTPRB</td>\n",
       "      <td>Receptor-type tyrosine-protein phosphatase beta</td>\n",
       "      <td>target</td>\n",
       "      <td>Humans</td>\n",
       "      <td>yes</td>\n",
       "      <td>inhibitor</td>\n",
       "      <td>HGNC:9665</td>\n",
       "      <td>investigational</td>\n",
       "      <td>5787</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>12999 rows × 9 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                       symbol  \\\n",
       "drugbank_id uniprot_id          \n",
       "DB00006     P00734         F2   \n",
       "DB00007     P30968      GNRHR   \n",
       "DB00014     P22888      LHCGR   \n",
       "            P30968      GNRHR   \n",
       "DB00035     P30518      AVPR2   \n",
       "...                       ...   \n",
       "DB15822     P21802      FGFR2   \n",
       "DB15873     P30874      SSTR2   \n",
       "DB15982     P03952      KLKB1   \n",
       "DB16019     P07288       KLK3   \n",
       "DB16353     P23467      PTPRB   \n",
       "\n",
       "                                                                   name  \\\n",
       "drugbank_id uniprot_id                                                    \n",
       "DB00006     P00734                                          Prothrombin   \n",
       "DB00007     P30968              Gonadotropin-releasing hormone receptor   \n",
       "DB00014     P22888         Lutropin-choriogonadotropic hormone receptor   \n",
       "            P30968              Gonadotropin-releasing hormone receptor   \n",
       "DB00035     P30518                              Vasopressin V2 receptor   \n",
       "...                                                                 ...   \n",
       "DB15822     P21802                  Fibroblast growth factor receptor 2   \n",
       "DB15873     P30874                         Somatostatin receptor type 2   \n",
       "DB15982     P03952                                    Plasma kallikrein   \n",
       "DB16019     P07288                            Prostate-specific antigen   \n",
       "DB16353     P23467      Receptor-type tyrosine-protein phosphatase beta   \n",
       "\n",
       "                       category organism known_action    actions     hgnc_id  \\\n",
       "drugbank_id uniprot_id                                                         \n",
       "DB00006     P00734       target   Humans          yes  inhibitor   HGNC:3535   \n",
       "DB00007     P30968       target   Humans          yes    agonist   HGNC:4421   \n",
       "DB00014     P22888       target   Humans          yes    agonist   HGNC:6585   \n",
       "            P30968       target   Humans          yes    agonist   HGNC:4421   \n",
       "DB00035     P30518       target   Humans          yes    agonist    HGNC:897   \n",
       "...                         ...      ...          ...        ...         ...   \n",
       "DB15822     P21802       target   Humans      unknown  inhibitor   HGNC:3689   \n",
       "DB15873     P30874       target   Humans          yes     binder  HGNC:11331   \n",
       "DB15982     P03952       target   Humans          yes  inhibitor   HGNC:6371   \n",
       "DB16019     P07288       target   Humans          yes     binder   HGNC:6364   \n",
       "DB16353     P23467       target   Humans          yes  inhibitor   HGNC:9665   \n",
       "\n",
       "                                  group entrez_id  \n",
       "drugbank_id uniprot_id                             \n",
       "DB00006     P00734             approved      2147  \n",
       "DB00007     P30968             approved      2798  \n",
       "DB00014     P22888             approved      3973  \n",
       "            P30968             approved      2798  \n",
       "DB00035     P30518             approved       554  \n",
       "...                                 ...       ...  \n",
       "DB15822     P21802             approved      2263  \n",
       "DB15873     P30874             approved      6752  \n",
       "DB15982     P03952             approved      3818  \n",
       "DB16019     P07288             approved       354  \n",
       "DB16353     P23467      investigational      5787  \n",
       "\n",
       "[12999 rows x 9 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "hgnc_fpath = '../../resources/hgnc/hgnc_complete_set.txt'\n",
    "proteins_f = repos_tools.extend_with_entrez_id(repos_tools.filter_drugbank_proteins(proteins, drugs), hgnc_fpath)\n",
    "proteins_f.to_csv('../../results/2021-08-11-drugbank/drugbank-filtered-proteins.csv')\n",
    "proteins_f"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "gothic-jerusalem",
   "metadata": {},
   "source": [
    "Collapse lines for a given drug"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "flying-finish",
   "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>entrez_id</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>drugbank_id</th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>DB00006</th>\n",
       "      <td>2147</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB00007</th>\n",
       "      <td>2798</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB00014</th>\n",
       "      <td>3973|2798</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB00035</th>\n",
       "      <td>554|552|553</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DB00050</th>\n",
       "      <td>2798|3973</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "               entrez_id\n",
       "drugbank_id             \n",
       "DB00006             2147\n",
       "DB00007             2798\n",
       "DB00014        3973|2798\n",
       "DB00035      554|552|553\n",
       "DB00050        2798|3973"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "entrez_ids = repos_tools.collapse_drugbank_proteins_group(proteins_f, col='entrez_id')\n",
    "entrez_ids.to_csv('../../results/2021-08-11-drugbank/drugbank-filtered-proteins-entrez_ids.csv')\n",
    "entrez_ids.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "insured-opposition",
   "metadata": {},
   "source": [
    "## Statistics"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "wrapped-noise",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['named-figure/drugbank-group-stats.png',\n",
       " 'named-figure/drugbank-group-stats.pdf']"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<Figure size 288x288 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "fig, ax = plt.subplots(figsize=(4, 4))\n",
    "proteins_f.groupby('drugbank_id').first().value_counts('group').plot(kind='barh', ax=ax)\n",
    "attila_utils.savefig(fig, 'drugbank-group-stats')"
   ]
  },
  {
   "cell_type": "raw",
   "id": "occupied-preview",
   "metadata": {},
   "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": 8,
   "id": "electoral-humanity",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{\n",
      "  \"shell_port\": 55947,\n",
      "  \"iopub_port\": 55948,\n",
      "  \"stdin_port\": 55949,\n",
      "  \"control_port\": 55951,\n",
      "  \"hb_port\": 55950,\n",
      "  \"ip\": \"127.0.0.1\",\n",
      "  \"key\": \"057f1b9c-91e65bb627bf23ec94266765\",\n",
      "  \"transport\": \"tcp\",\n",
      "  \"signature_scheme\": \"hmac-sha256\",\n",
      "  \"kernel_name\": \"\"\n",
      "}\n",
      "\n",
      "Paste the above JSON into a file, and connect with:\n",
      "    $> jupyter <app> --existing <file>\n",
      "or, if you are local, you can connect with just:\n",
      "    $> jupyter <app> --existing kernel-3a1d13fa-bf79-424c-80de-2a43a54e0949.json\n",
      "or even just:\n",
      "    $> jupyter <app> --existing\n",
      "if this is the most recent Jupyter kernel you have started.\n"
     ]
    }
   ],
   "source": [
    "%connect_info"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "super-survival",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.8.8"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}