bioactivity-data.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Bioactivity data mining for drug discovery using ChEMBL "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Install the ChEMBL web service package to retrieve bioactivity data from ChEMBL Database"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Requirement already satisfied: chembl_webresource_client in c:\\users\\cmkin\\anaconda3\\lib\\site-packages (0.10.7)\n",
      "Requirement already satisfied: requests>=2.18.4 in c:\\users\\cmkin\\anaconda3\\lib\\site-packages (from chembl_webresource_client) (2.26.0)\n",
      "Requirement already satisfied: easydict in c:\\users\\cmkin\\anaconda3\\lib\\site-packages (from chembl_webresource_client) (1.9)\n",
      "Requirement already satisfied: urllib3 in c:\\users\\cmkin\\anaconda3\\lib\\site-packages (from chembl_webresource_client) (1.26.7)\n",
      "Requirement already satisfied: requests-cache~=0.7.0 in c:\\users\\cmkin\\anaconda3\\lib\\site-packages (from chembl_webresource_client) (0.7.5)\n",
      "Requirement already satisfied: certifi>=2017.4.17 in c:\\users\\cmkin\\anaconda3\\lib\\site-packages (from requests>=2.18.4->chembl_webresource_client) (2021.10.8)\n",
      "Requirement already satisfied: charset-normalizer~=2.0.0 in c:\\users\\cmkin\\anaconda3\\lib\\site-packages (from requests>=2.18.4->chembl_webresource_client) (2.0.4)\n",
      "Requirement already satisfied: idna<4,>=2.5 in c:\\users\\cmkin\\anaconda3\\lib\\site-packages (from requests>=2.18.4->chembl_webresource_client) (3.2)\n",
      "Requirement already satisfied: attrs<22.0,>=21.2 in c:\\users\\cmkin\\anaconda3\\lib\\site-packages (from requests-cache~=0.7.0->chembl_webresource_client) (21.2.0)\n",
      "Requirement already satisfied: url-normalize<2.0,>=1.4 in c:\\users\\cmkin\\anaconda3\\lib\\site-packages (from requests-cache~=0.7.0->chembl_webresource_client) (1.4.3)\n",
      "Requirement already satisfied: pyyaml>=5.4 in c:\\users\\cmkin\\anaconda3\\lib\\site-packages (from requests-cache~=0.7.0->chembl_webresource_client) (6.0)\n",
      "Requirement already satisfied: itsdangerous>=2.0.1 in c:\\users\\cmkin\\anaconda3\\lib\\site-packages (from requests-cache~=0.7.0->chembl_webresource_client) (2.0.1)\n",
      "Requirement already satisfied: six in c:\\users\\cmkin\\anaconda3\\lib\\site-packages (from url-normalize<2.0,>=1.4->requests-cache~=0.7.0->chembl_webresource_client) (1.16.0)\n"
     ]
    }
   ],
   "source": [
    "# install libraries\n",
    "! pip install chembl_webresource_client"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "from chembl_webresource_client.new_client import new_client"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Search for target protein"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "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>cross_references</th>\n",
       "      <th>organism</th>\n",
       "      <th>pref_name</th>\n",
       "      <th>score</th>\n",
       "      <th>species_group_flag</th>\n",
       "      <th>target_chembl_id</th>\n",
       "      <th>target_components</th>\n",
       "      <th>target_type</th>\n",
       "      <th>tax_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>[{'xref_id': 'Q01279', 'xref_name': None, 'xre...</td>\n",
       "      <td>Mus musculus</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>16.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL3608</td>\n",
       "      <td>[{'accession': 'Q01279', 'component_descriptio...</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>10090</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>[]</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>EGFR/PPP1CA</td>\n",
       "      <td>16.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL4523747</td>\n",
       "      <td>[{'accession': 'P00533', 'component_descriptio...</td>\n",
       "      <td>PROTEIN-PROTEIN INTERACTION</td>\n",
       "      <td>9606</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>[]</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>VHL/EGFR</td>\n",
       "      <td>16.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL4523998</td>\n",
       "      <td>[{'accession': 'P00533', 'component_descriptio...</td>\n",
       "      <td>PROTEIN-PROTEIN INTERACTION</td>\n",
       "      <td>9606</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>[{'xref_id': 'P00533', 'xref_name': None, 'xre...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>12.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL203</td>\n",
       "      <td>[{'accession': 'P00533', 'component_descriptio...</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>9606</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>[]</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Protein cereblon/Epidermal growth factor receptor</td>\n",
       "      <td>11.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL4523680</td>\n",
       "      <td>[{'accession': 'P00533', 'component_descriptio...</td>\n",
       "      <td>PROTEIN-PROTEIN INTERACTION</td>\n",
       "      <td>9606</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>[]</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>MER intracellular domain/EGFR extracellular do...</td>\n",
       "      <td>9.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL3137284</td>\n",
       "      <td>[{'accession': 'P00533', 'component_descriptio...</td>\n",
       "      <td>CHIMERIC PROTEIN</td>\n",
       "      <td>9606</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>[]</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor and ErbB2 (HE...</td>\n",
       "      <td>7.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL2111431</td>\n",
       "      <td>[{'accession': 'P04626', 'component_descriptio...</td>\n",
       "      <td>PROTEIN FAMILY</td>\n",
       "      <td>9606</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>[]</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Baculoviral IAP repeat-containing protein 2/Ep...</td>\n",
       "      <td>7.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL4802031</td>\n",
       "      <td>[{'accession': 'P00533', 'component_descriptio...</td>\n",
       "      <td>PROTEIN-PROTEIN INTERACTION</td>\n",
       "      <td>9606</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>[]</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor</td>\n",
       "      <td>5.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL2363049</td>\n",
       "      <td>[{'accession': 'P04626', 'component_descriptio...</td>\n",
       "      <td>PROTEIN FAMILY</td>\n",
       "      <td>9606</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                    cross_references      organism  \\\n",
       "0  [{'xref_id': 'Q01279', 'xref_name': None, 'xre...  Mus musculus   \n",
       "1                                                 []  Homo sapiens   \n",
       "2                                                 []  Homo sapiens   \n",
       "3  [{'xref_id': 'P00533', 'xref_name': None, 'xre...  Homo sapiens   \n",
       "4                                                 []  Homo sapiens   \n",
       "5                                                 []  Homo sapiens   \n",
       "6                                                 []  Homo sapiens   \n",
       "7                                                 []  Homo sapiens   \n",
       "8                                                 []  Homo sapiens   \n",
       "\n",
       "                                           pref_name  score  \\\n",
       "0             Epidermal growth factor receptor erbB1   16.0   \n",
       "1                                        EGFR/PPP1CA   16.0   \n",
       "2                                           VHL/EGFR   16.0   \n",
       "3             Epidermal growth factor receptor erbB1   12.0   \n",
       "4  Protein cereblon/Epidermal growth factor receptor   11.0   \n",
       "5  MER intracellular domain/EGFR extracellular do...    9.0   \n",
       "6  Epidermal growth factor receptor and ErbB2 (HE...    7.0   \n",
       "7  Baculoviral IAP repeat-containing protein 2/Ep...    7.0   \n",
       "8                   Epidermal growth factor receptor    5.0   \n",
       "\n",
       "   species_group_flag target_chembl_id  \\\n",
       "0               False       CHEMBL3608   \n",
       "1               False    CHEMBL4523747   \n",
       "2               False    CHEMBL4523998   \n",
       "3               False        CHEMBL203   \n",
       "4               False    CHEMBL4523680   \n",
       "5               False    CHEMBL3137284   \n",
       "6               False    CHEMBL2111431   \n",
       "7               False    CHEMBL4802031   \n",
       "8               False    CHEMBL2363049   \n",
       "\n",
       "                                   target_components  \\\n",
       "0  [{'accession': 'Q01279', 'component_descriptio...   \n",
       "1  [{'accession': 'P00533', 'component_descriptio...   \n",
       "2  [{'accession': 'P00533', 'component_descriptio...   \n",
       "3  [{'accession': 'P00533', 'component_descriptio...   \n",
       "4  [{'accession': 'P00533', 'component_descriptio...   \n",
       "5  [{'accession': 'P00533', 'component_descriptio...   \n",
       "6  [{'accession': 'P04626', 'component_descriptio...   \n",
       "7  [{'accession': 'P00533', 'component_descriptio...   \n",
       "8  [{'accession': 'P04626', 'component_descriptio...   \n",
       "\n",
       "                   target_type  tax_id  \n",
       "0               SINGLE PROTEIN   10090  \n",
       "1  PROTEIN-PROTEIN INTERACTION    9606  \n",
       "2  PROTEIN-PROTEIN INTERACTION    9606  \n",
       "3               SINGLE PROTEIN    9606  \n",
       "4  PROTEIN-PROTEIN INTERACTION    9606  \n",
       "5             CHIMERIC PROTEIN    9606  \n",
       "6               PROTEIN FAMILY    9606  \n",
       "7  PROTEIN-PROTEIN INTERACTION    9606  \n",
       "8               PROTEIN FAMILY    9606  "
      ]
     },
     "execution_count": 40,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# test case: EGFR\n",
    "target = new_client.target\n",
    "target_query = target.search('EGFR')\n",
    "targets = pd.DataFrame.from_dict(target_query)\n",
    "targets"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Select and retrieve bioactivity data "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'CHEMBL203'"
      ]
     },
     "execution_count": 41,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# select the target of interest from the search results\n",
    "selected_target = targets.target_chembl_id[3]\n",
    "selected_target"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Filter results to retrieve only bioactivity data for protein of interest that are reported as IC50 values in nM units"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "metadata": {},
   "outputs": [],
   "source": [
    "activity = new_client.activity\n",
    "res = activity.filter(target_chembl_id=selected_target).filter(standard_type=\"IC50\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "metadata": {},
   "outputs": [],
   "source": [
    "df = pd.DataFrame.from_dict(res)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>activity_comment</th>\n",
       "      <th>activity_id</th>\n",
       "      <th>activity_properties</th>\n",
       "      <th>assay_chembl_id</th>\n",
       "      <th>assay_description</th>\n",
       "      <th>assay_type</th>\n",
       "      <th>assay_variant_accession</th>\n",
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       "      <th>bao_endpoint</th>\n",
       "      <th>bao_format</th>\n",
       "      <th>...</th>\n",
       "      <th>target_organism</th>\n",
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       "      <th>text_value</th>\n",
       "      <th>toid</th>\n",
       "      <th>type</th>\n",
       "      <th>units</th>\n",
       "      <th>uo_units</th>\n",
       "      <th>upper_value</th>\n",
       "      <th>value</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
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       "      <th>0</th>\n",
       "      <td>None</td>\n",
       "      <td>32260</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL674637</td>\n",
       "      <td>Inhibitory activity towards tyrosine phosphory...</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.041</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>None</td>\n",
       "      <td>32263</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL621151</td>\n",
       "      <td>Inhibition of autophosphorylation of human epi...</td>\n",
       "      <td>F</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000219</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>None</td>\n",
       "      <td>32265</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL615325</td>\n",
       "      <td>Inhibition of ligand-induced proliferation in ...</td>\n",
       "      <td>F</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000219</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>7.82</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>None</td>\n",
       "      <td>32267</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL674637</td>\n",
       "      <td>Inhibitory activity towards tyrosine phosphory...</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.17</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>None</td>\n",
       "      <td>32270</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL621151</td>\n",
       "      <td>Inhibition of autophosphorylation of human epi...</td>\n",
       "      <td>F</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000219</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.04</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",
       "      <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>15258</th>\n",
       "      <td>Not Active</td>\n",
       "      <td>23070040</td>\n",
       "      <td>[{'comments': None, 'relation': None, 'result_...</td>\n",
       "      <td>CHEMBL4509084</td>\n",
       "      <td>EGFR kinase inhibition assay</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000179</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>µM</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>20.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15259</th>\n",
       "      <td>None</td>\n",
       "      <td>23090818</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL4510669</td>\n",
       "      <td>Protein Tyrosine Kinase, EGF Receptor Eurofins...</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000179</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>µM</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>4.59</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15260</th>\n",
       "      <td>None</td>\n",
       "      <td>23116071</td>\n",
       "      <td>[{'comments': None, 'relation': None, 'result_...</td>\n",
       "      <td>CHEMBL4512500</td>\n",
       "      <td>EGFR(EGFRMGB1) Takeda global kinase panel</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000179</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>pIC50</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>6.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15261</th>\n",
       "      <td>None</td>\n",
       "      <td>23116480</td>\n",
       "      <td>[{'comments': None, 'relation': None, 'result_...</td>\n",
       "      <td>CHEMBL4512213</td>\n",
       "      <td>EGFR(EGFRMGB1) Takeda global kinase panel</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000179</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>pIC50</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>6.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15262</th>\n",
       "      <td>None</td>\n",
       "      <td>23116841</td>\n",
       "      <td>[{'comments': None, 'relation': None, 'result_...</td>\n",
       "      <td>CHEMBL4512787</td>\n",
       "      <td>EGFR(EGFRMGB1) Takeda global kinase panel</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000179</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>pIC50</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>6.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>15263 rows × 45 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      activity_comment  activity_id  \\\n",
       "0                 None        32260   \n",
       "1                 None        32263   \n",
       "2                 None        32265   \n",
       "3                 None        32267   \n",
       "4                 None        32270   \n",
       "...                ...          ...   \n",
       "15258       Not Active     23070040   \n",
       "15259             None     23090818   \n",
       "15260             None     23116071   \n",
       "15261             None     23116480   \n",
       "15262             None     23116841   \n",
       "\n",
       "                                     activity_properties assay_chembl_id  \\\n",
       "0                                                     []    CHEMBL674637   \n",
       "1                                                     []    CHEMBL621151   \n",
       "2                                                     []    CHEMBL615325   \n",
       "3                                                     []    CHEMBL674637   \n",
       "4                                                     []    CHEMBL621151   \n",
       "...                                                  ...             ...   \n",
       "15258  [{'comments': None, 'relation': None, 'result_...   CHEMBL4509084   \n",
       "15259                                                 []   CHEMBL4510669   \n",
       "15260  [{'comments': None, 'relation': None, 'result_...   CHEMBL4512500   \n",
       "15261  [{'comments': None, 'relation': None, 'result_...   CHEMBL4512213   \n",
       "15262  [{'comments': None, 'relation': None, 'result_...   CHEMBL4512787   \n",
       "\n",
       "                                       assay_description assay_type  \\\n",
       "0      Inhibitory activity towards tyrosine phosphory...          B   \n",
       "1      Inhibition of autophosphorylation of human epi...          F   \n",
       "2      Inhibition of ligand-induced proliferation in ...          F   \n",
       "3      Inhibitory activity towards tyrosine phosphory...          B   \n",
       "4      Inhibition of autophosphorylation of human epi...          F   \n",
       "...                                                  ...        ...   \n",
       "15258                       EGFR kinase inhibition assay          B   \n",
       "15259  Protein Tyrosine Kinase, EGF Receptor Eurofins...          B   \n",
       "15260          EGFR(EGFRMGB1) Takeda global kinase panel          B   \n",
       "15261          EGFR(EGFRMGB1) Takeda global kinase panel          B   \n",
       "15262          EGFR(EGFRMGB1) Takeda global kinase panel          B   \n",
       "\n",
       "      assay_variant_accession assay_variant_mutation bao_endpoint  \\\n",
       "0                        None                   None  BAO_0000190   \n",
       "1                        None                   None  BAO_0000190   \n",
       "2                        None                   None  BAO_0000190   \n",
       "3                        None                   None  BAO_0000190   \n",
       "4                        None                   None  BAO_0000190   \n",
       "...                       ...                    ...          ...   \n",
       "15258                    None                   None  BAO_0000179   \n",
       "15259                    None                   None  BAO_0000179   \n",
       "15260                    None                   None  BAO_0000179   \n",
       "15261                    None                   None  BAO_0000179   \n",
       "15262                    None                   None  BAO_0000179   \n",
       "\n",
       "        bao_format  ... target_organism  \\\n",
       "0      BAO_0000357  ...    Homo sapiens   \n",
       "1      BAO_0000219  ...    Homo sapiens   \n",
       "2      BAO_0000219  ...    Homo sapiens   \n",
       "3      BAO_0000357  ...    Homo sapiens   \n",
       "4      BAO_0000219  ...    Homo sapiens   \n",
       "...            ...  ...             ...   \n",
       "15258  BAO_0000357  ...    Homo sapiens   \n",
       "15259  BAO_0000357  ...    Homo sapiens   \n",
       "15260  BAO_0000357  ...    Homo sapiens   \n",
       "15261  BAO_0000357  ...    Homo sapiens   \n",
       "15262  BAO_0000357  ...    Homo sapiens   \n",
       "\n",
       "                             target_pref_name target_tax_id text_value  toid  \\\n",
       "0      Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "1      Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "2      Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "3      Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "4      Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "...                                       ...           ...        ...   ...   \n",
       "15258  Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "15259  Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "15260  Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "15261  Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "15262  Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "\n",
       "        type  units    uo_units upper_value  value  \n",
       "0       IC50     uM  UO_0000065        None  0.041  \n",
       "1       IC50     uM  UO_0000065        None    0.3  \n",
       "2       IC50     uM  UO_0000065        None   7.82  \n",
       "3       IC50     uM  UO_0000065        None   0.17  \n",
       "4       IC50     uM  UO_0000065        None   0.04  \n",
       "...      ...    ...         ...         ...    ...  \n",
       "15258   IC50     µM        None        None   20.0  \n",
       "15259   IC50     µM        None        None   4.59  \n",
       "15260  pIC50   None        None        None    6.0  \n",
       "15261  pIC50   None        None        None    6.0  \n",
       "15262  pIC50   None        None        None    6.0  \n",
       "\n",
       "[15263 rows x 45 columns]"
      ]
     },
     "execution_count": 44,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 45,
   "metadata": {},
   "outputs": [],
   "source": [
    "df.to_csv('EGFR_01_bioactivity_data_raw.csv', index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "metadata": {},
   "outputs": [],
   "source": [
    "df = pd.DataFrame.from_dict(res)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "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",
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       "    .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>activity_comment</th>\n",
       "      <th>activity_id</th>\n",
       "      <th>activity_properties</th>\n",
       "      <th>assay_chembl_id</th>\n",
       "      <th>assay_description</th>\n",
       "      <th>assay_type</th>\n",
       "      <th>assay_variant_accession</th>\n",
       "      <th>assay_variant_mutation</th>\n",
       "      <th>bao_endpoint</th>\n",
       "      <th>bao_format</th>\n",
       "      <th>...</th>\n",
       "      <th>target_organism</th>\n",
       "      <th>target_pref_name</th>\n",
       "      <th>target_tax_id</th>\n",
       "      <th>text_value</th>\n",
       "      <th>toid</th>\n",
       "      <th>type</th>\n",
       "      <th>units</th>\n",
       "      <th>uo_units</th>\n",
       "      <th>upper_value</th>\n",
       "      <th>value</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>None</td>\n",
       "      <td>32260</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL674637</td>\n",
       "      <td>Inhibitory activity towards tyrosine phosphory...</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.041</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>None</td>\n",
       "      <td>32263</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL621151</td>\n",
       "      <td>Inhibition of autophosphorylation of human epi...</td>\n",
       "      <td>F</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000219</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>None</td>\n",
       "      <td>32265</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL615325</td>\n",
       "      <td>Inhibition of ligand-induced proliferation in ...</td>\n",
       "      <td>F</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000219</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>7.82</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>None</td>\n",
       "      <td>32267</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL674637</td>\n",
       "      <td>Inhibitory activity towards tyrosine phosphory...</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.17</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>None</td>\n",
       "      <td>32270</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL621151</td>\n",
       "      <td>Inhibition of autophosphorylation of human epi...</td>\n",
       "      <td>F</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000219</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.04</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",
       "      <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>15258</th>\n",
       "      <td>Not Active</td>\n",
       "      <td>23070040</td>\n",
       "      <td>[{'comments': None, 'relation': None, 'result_...</td>\n",
       "      <td>CHEMBL4509084</td>\n",
       "      <td>EGFR kinase inhibition assay</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000179</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>µM</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>20.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15259</th>\n",
       "      <td>None</td>\n",
       "      <td>23090818</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL4510669</td>\n",
       "      <td>Protein Tyrosine Kinase, EGF Receptor Eurofins...</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000179</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>µM</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>4.59</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15260</th>\n",
       "      <td>None</td>\n",
       "      <td>23116071</td>\n",
       "      <td>[{'comments': None, 'relation': None, 'result_...</td>\n",
       "      <td>CHEMBL4512500</td>\n",
       "      <td>EGFR(EGFRMGB1) Takeda global kinase panel</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000179</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>pIC50</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>6.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15261</th>\n",
       "      <td>None</td>\n",
       "      <td>23116480</td>\n",
       "      <td>[{'comments': None, 'relation': None, 'result_...</td>\n",
       "      <td>CHEMBL4512213</td>\n",
       "      <td>EGFR(EGFRMGB1) Takeda global kinase panel</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000179</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>pIC50</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>6.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15262</th>\n",
       "      <td>None</td>\n",
       "      <td>23116841</td>\n",
       "      <td>[{'comments': None, 'relation': None, 'result_...</td>\n",
       "      <td>CHEMBL4512787</td>\n",
       "      <td>EGFR(EGFRMGB1) Takeda global kinase panel</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000179</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>pIC50</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>6.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>15263 rows × 45 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      activity_comment  activity_id  \\\n",
       "0                 None        32260   \n",
       "1                 None        32263   \n",
       "2                 None        32265   \n",
       "3                 None        32267   \n",
       "4                 None        32270   \n",
       "...                ...          ...   \n",
       "15258       Not Active     23070040   \n",
       "15259             None     23090818   \n",
       "15260             None     23116071   \n",
       "15261             None     23116480   \n",
       "15262             None     23116841   \n",
       "\n",
       "                                     activity_properties assay_chembl_id  \\\n",
       "0                                                     []    CHEMBL674637   \n",
       "1                                                     []    CHEMBL621151   \n",
       "2                                                     []    CHEMBL615325   \n",
       "3                                                     []    CHEMBL674637   \n",
       "4                                                     []    CHEMBL621151   \n",
       "...                                                  ...             ...   \n",
       "15258  [{'comments': None, 'relation': None, 'result_...   CHEMBL4509084   \n",
       "15259                                                 []   CHEMBL4510669   \n",
       "15260  [{'comments': None, 'relation': None, 'result_...   CHEMBL4512500   \n",
       "15261  [{'comments': None, 'relation': None, 'result_...   CHEMBL4512213   \n",
       "15262  [{'comments': None, 'relation': None, 'result_...   CHEMBL4512787   \n",
       "\n",
       "                                       assay_description assay_type  \\\n",
       "0      Inhibitory activity towards tyrosine phosphory...          B   \n",
       "1      Inhibition of autophosphorylation of human epi...          F   \n",
       "2      Inhibition of ligand-induced proliferation in ...          F   \n",
       "3      Inhibitory activity towards tyrosine phosphory...          B   \n",
       "4      Inhibition of autophosphorylation of human epi...          F   \n",
       "...                                                  ...        ...   \n",
       "15258                       EGFR kinase inhibition assay          B   \n",
       "15259  Protein Tyrosine Kinase, EGF Receptor Eurofins...          B   \n",
       "15260          EGFR(EGFRMGB1) Takeda global kinase panel          B   \n",
       "15261          EGFR(EGFRMGB1) Takeda global kinase panel          B   \n",
       "15262          EGFR(EGFRMGB1) Takeda global kinase panel          B   \n",
       "\n",
       "      assay_variant_accession assay_variant_mutation bao_endpoint  \\\n",
       "0                        None                   None  BAO_0000190   \n",
       "1                        None                   None  BAO_0000190   \n",
       "2                        None                   None  BAO_0000190   \n",
       "3                        None                   None  BAO_0000190   \n",
       "4                        None                   None  BAO_0000190   \n",
       "...                       ...                    ...          ...   \n",
       "15258                    None                   None  BAO_0000179   \n",
       "15259                    None                   None  BAO_0000179   \n",
       "15260                    None                   None  BAO_0000179   \n",
       "15261                    None                   None  BAO_0000179   \n",
       "15262                    None                   None  BAO_0000179   \n",
       "\n",
       "        bao_format  ... target_organism  \\\n",
       "0      BAO_0000357  ...    Homo sapiens   \n",
       "1      BAO_0000219  ...    Homo sapiens   \n",
       "2      BAO_0000219  ...    Homo sapiens   \n",
       "3      BAO_0000357  ...    Homo sapiens   \n",
       "4      BAO_0000219  ...    Homo sapiens   \n",
       "...            ...  ...             ...   \n",
       "15258  BAO_0000357  ...    Homo sapiens   \n",
       "15259  BAO_0000357  ...    Homo sapiens   \n",
       "15260  BAO_0000357  ...    Homo sapiens   \n",
       "15261  BAO_0000357  ...    Homo sapiens   \n",
       "15262  BAO_0000357  ...    Homo sapiens   \n",
       "\n",
       "                             target_pref_name target_tax_id text_value  toid  \\\n",
       "0      Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "1      Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "2      Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "3      Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "4      Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "...                                       ...           ...        ...   ...   \n",
       "15258  Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "15259  Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "15260  Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "15261  Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "15262  Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "\n",
       "        type  units    uo_units upper_value  value  \n",
       "0       IC50     uM  UO_0000065        None  0.041  \n",
       "1       IC50     uM  UO_0000065        None    0.3  \n",
       "2       IC50     uM  UO_0000065        None   7.82  \n",
       "3       IC50     uM  UO_0000065        None   0.17  \n",
       "4       IC50     uM  UO_0000065        None   0.04  \n",
       "...      ...    ...         ...         ...    ...  \n",
       "15258   IC50     µM        None        None   20.0  \n",
       "15259   IC50     µM        None        None   4.59  \n",
       "15260  pIC50   None        None        None    6.0  \n",
       "15261  pIC50   None        None        None    6.0  \n",
       "15262  pIC50   None        None        None    6.0  \n",
       "\n",
       "[15263 rows x 45 columns]"
      ]
     },
     "execution_count": 47,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "metadata": {},
   "outputs": [],
   "source": [
    "df.to_csv('EGFR_01_bioactivity_data_raw.csv', index=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Handling missing data"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Exclude any compound that has missing value for the standard_value column"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 49,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "C:\\Users\\cmkin\\AppData\\Local\\Temp/ipykernel_15272/3852201246.py:2: UserWarning: Boolean Series key will be reindexed to match DataFrame index.\n",
      "  df2 = df2[df.canonical_smiles.notna()]\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
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       "    }\n",
       "\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>activity_comment</th>\n",
       "      <th>activity_id</th>\n",
       "      <th>activity_properties</th>\n",
       "      <th>assay_chembl_id</th>\n",
       "      <th>assay_description</th>\n",
       "      <th>assay_type</th>\n",
       "      <th>assay_variant_accession</th>\n",
       "      <th>assay_variant_mutation</th>\n",
       "      <th>bao_endpoint</th>\n",
       "      <th>bao_format</th>\n",
       "      <th>...</th>\n",
       "      <th>target_organism</th>\n",
       "      <th>target_pref_name</th>\n",
       "      <th>target_tax_id</th>\n",
       "      <th>text_value</th>\n",
       "      <th>toid</th>\n",
       "      <th>type</th>\n",
       "      <th>units</th>\n",
       "      <th>uo_units</th>\n",
       "      <th>upper_value</th>\n",
       "      <th>value</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>None</td>\n",
       "      <td>32260</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL674637</td>\n",
       "      <td>Inhibitory activity towards tyrosine phosphory...</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.041</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>None</td>\n",
       "      <td>32263</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL621151</td>\n",
       "      <td>Inhibition of autophosphorylation of human epi...</td>\n",
       "      <td>F</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000219</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>None</td>\n",
       "      <td>32265</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL615325</td>\n",
       "      <td>Inhibition of ligand-induced proliferation in ...</td>\n",
       "      <td>F</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000219</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>7.82</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>None</td>\n",
       "      <td>32267</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL674637</td>\n",
       "      <td>Inhibitory activity towards tyrosine phosphory...</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.17</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>None</td>\n",
       "      <td>32270</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL621151</td>\n",
       "      <td>Inhibition of autophosphorylation of human epi...</td>\n",
       "      <td>F</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000219</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.04</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",
       "      <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>15258</th>\n",
       "      <td>Not Active</td>\n",
       "      <td>23070040</td>\n",
       "      <td>[{'comments': None, 'relation': None, 'result_...</td>\n",
       "      <td>CHEMBL4509084</td>\n",
       "      <td>EGFR kinase inhibition assay</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000179</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>µM</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>20.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15259</th>\n",
       "      <td>None</td>\n",
       "      <td>23090818</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL4510669</td>\n",
       "      <td>Protein Tyrosine Kinase, EGF Receptor Eurofins...</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000179</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>µM</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>4.59</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15260</th>\n",
       "      <td>None</td>\n",
       "      <td>23116071</td>\n",
       "      <td>[{'comments': None, 'relation': None, 'result_...</td>\n",
       "      <td>CHEMBL4512500</td>\n",
       "      <td>EGFR(EGFRMGB1) Takeda global kinase panel</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000179</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>pIC50</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>6.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15261</th>\n",
       "      <td>None</td>\n",
       "      <td>23116480</td>\n",
       "      <td>[{'comments': None, 'relation': None, 'result_...</td>\n",
       "      <td>CHEMBL4512213</td>\n",
       "      <td>EGFR(EGFRMGB1) Takeda global kinase panel</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000179</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>pIC50</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>6.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15262</th>\n",
       "      <td>None</td>\n",
       "      <td>23116841</td>\n",
       "      <td>[{'comments': None, 'relation': None, 'result_...</td>\n",
       "      <td>CHEMBL4512787</td>\n",
       "      <td>EGFR(EGFRMGB1) Takeda global kinase panel</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000179</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>pIC50</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>6.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>13897 rows × 45 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      activity_comment  activity_id  \\\n",
       "0                 None        32260   \n",
       "1                 None        32263   \n",
       "2                 None        32265   \n",
       "3                 None        32267   \n",
       "4                 None        32270   \n",
       "...                ...          ...   \n",
       "15258       Not Active     23070040   \n",
       "15259             None     23090818   \n",
       "15260             None     23116071   \n",
       "15261             None     23116480   \n",
       "15262             None     23116841   \n",
       "\n",
       "                                     activity_properties assay_chembl_id  \\\n",
       "0                                                     []    CHEMBL674637   \n",
       "1                                                     []    CHEMBL621151   \n",
       "2                                                     []    CHEMBL615325   \n",
       "3                                                     []    CHEMBL674637   \n",
       "4                                                     []    CHEMBL621151   \n",
       "...                                                  ...             ...   \n",
       "15258  [{'comments': None, 'relation': None, 'result_...   CHEMBL4509084   \n",
       "15259                                                 []   CHEMBL4510669   \n",
       "15260  [{'comments': None, 'relation': None, 'result_...   CHEMBL4512500   \n",
       "15261  [{'comments': None, 'relation': None, 'result_...   CHEMBL4512213   \n",
       "15262  [{'comments': None, 'relation': None, 'result_...   CHEMBL4512787   \n",
       "\n",
       "                                       assay_description assay_type  \\\n",
       "0      Inhibitory activity towards tyrosine phosphory...          B   \n",
       "1      Inhibition of autophosphorylation of human epi...          F   \n",
       "2      Inhibition of ligand-induced proliferation in ...          F   \n",
       "3      Inhibitory activity towards tyrosine phosphory...          B   \n",
       "4      Inhibition of autophosphorylation of human epi...          F   \n",
       "...                                                  ...        ...   \n",
       "15258                       EGFR kinase inhibition assay          B   \n",
       "15259  Protein Tyrosine Kinase, EGF Receptor Eurofins...          B   \n",
       "15260          EGFR(EGFRMGB1) Takeda global kinase panel          B   \n",
       "15261          EGFR(EGFRMGB1) Takeda global kinase panel          B   \n",
       "15262          EGFR(EGFRMGB1) Takeda global kinase panel          B   \n",
       "\n",
       "      assay_variant_accession assay_variant_mutation bao_endpoint  \\\n",
       "0                        None                   None  BAO_0000190   \n",
       "1                        None                   None  BAO_0000190   \n",
       "2                        None                   None  BAO_0000190   \n",
       "3                        None                   None  BAO_0000190   \n",
       "4                        None                   None  BAO_0000190   \n",
       "...                       ...                    ...          ...   \n",
       "15258                    None                   None  BAO_0000179   \n",
       "15259                    None                   None  BAO_0000179   \n",
       "15260                    None                   None  BAO_0000179   \n",
       "15261                    None                   None  BAO_0000179   \n",
       "15262                    None                   None  BAO_0000179   \n",
       "\n",
       "        bao_format  ... target_organism  \\\n",
       "0      BAO_0000357  ...    Homo sapiens   \n",
       "1      BAO_0000219  ...    Homo sapiens   \n",
       "2      BAO_0000219  ...    Homo sapiens   \n",
       "3      BAO_0000357  ...    Homo sapiens   \n",
       "4      BAO_0000219  ...    Homo sapiens   \n",
       "...            ...  ...             ...   \n",
       "15258  BAO_0000357  ...    Homo sapiens   \n",
       "15259  BAO_0000357  ...    Homo sapiens   \n",
       "15260  BAO_0000357  ...    Homo sapiens   \n",
       "15261  BAO_0000357  ...    Homo sapiens   \n",
       "15262  BAO_0000357  ...    Homo sapiens   \n",
       "\n",
       "                             target_pref_name target_tax_id text_value  toid  \\\n",
       "0      Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "1      Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "2      Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "3      Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "4      Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "...                                       ...           ...        ...   ...   \n",
       "15258  Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "15259  Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "15260  Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "15261  Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "15262  Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "\n",
       "        type  units    uo_units upper_value  value  \n",
       "0       IC50     uM  UO_0000065        None  0.041  \n",
       "1       IC50     uM  UO_0000065        None    0.3  \n",
       "2       IC50     uM  UO_0000065        None   7.82  \n",
       "3       IC50     uM  UO_0000065        None   0.17  \n",
       "4       IC50     uM  UO_0000065        None   0.04  \n",
       "...      ...    ...         ...         ...    ...  \n",
       "15258   IC50     µM        None        None   20.0  \n",
       "15259   IC50     µM        None        None   4.59  \n",
       "15260  pIC50   None        None        None    6.0  \n",
       "15261  pIC50   None        None        None    6.0  \n",
       "15262  pIC50   None        None        None    6.0  \n",
       "\n",
       "[13897 rows x 45 columns]"
      ]
     },
     "execution_count": 49,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df2 = df[df.standard_value.notna()]\n",
    "df2 = df2[df.canonical_smiles.notna()]\n",
    "df2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "8915"
      ]
     },
     "execution_count": 50,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(df2.canonical_smiles.unique())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "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>activity_comment</th>\n",
       "      <th>activity_id</th>\n",
       "      <th>activity_properties</th>\n",
       "      <th>assay_chembl_id</th>\n",
       "      <th>assay_description</th>\n",
       "      <th>assay_type</th>\n",
       "      <th>assay_variant_accession</th>\n",
       "      <th>assay_variant_mutation</th>\n",
       "      <th>bao_endpoint</th>\n",
       "      <th>bao_format</th>\n",
       "      <th>...</th>\n",
       "      <th>target_organism</th>\n",
       "      <th>target_pref_name</th>\n",
       "      <th>target_tax_id</th>\n",
       "      <th>text_value</th>\n",
       "      <th>toid</th>\n",
       "      <th>type</th>\n",
       "      <th>units</th>\n",
       "      <th>uo_units</th>\n",
       "      <th>upper_value</th>\n",
       "      <th>value</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>None</td>\n",
       "      <td>32260</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL674637</td>\n",
       "      <td>Inhibitory activity towards tyrosine phosphory...</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.041</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>None</td>\n",
       "      <td>32267</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL674637</td>\n",
       "      <td>Inhibitory activity towards tyrosine phosphory...</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.17</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>None</td>\n",
       "      <td>32680</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL677833</td>\n",
       "      <td>In vitro inhibition of Epidermal growth factor...</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>9.3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>None</td>\n",
       "      <td>32770</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL674643</td>\n",
       "      <td>Inhibitory concentration of EGF dependent auto...</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>500.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>None</td>\n",
       "      <td>32772</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL674643</td>\n",
       "      <td>Inhibitory concentration of EGF dependent auto...</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>3000.0</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",
       "      <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>15258</th>\n",
       "      <td>Not Active</td>\n",
       "      <td>23070040</td>\n",
       "      <td>[{'comments': None, 'relation': None, 'result_...</td>\n",
       "      <td>CHEMBL4509084</td>\n",
       "      <td>EGFR kinase inhibition assay</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000179</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>µM</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>20.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15259</th>\n",
       "      <td>None</td>\n",
       "      <td>23090818</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL4510669</td>\n",
       "      <td>Protein Tyrosine Kinase, EGF Receptor Eurofins...</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000179</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>µM</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>4.59</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15260</th>\n",
       "      <td>None</td>\n",
       "      <td>23116071</td>\n",
       "      <td>[{'comments': None, 'relation': None, 'result_...</td>\n",
       "      <td>CHEMBL4512500</td>\n",
       "      <td>EGFR(EGFRMGB1) Takeda global kinase panel</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000179</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>pIC50</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>6.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15261</th>\n",
       "      <td>None</td>\n",
       "      <td>23116480</td>\n",
       "      <td>[{'comments': None, 'relation': None, 'result_...</td>\n",
       "      <td>CHEMBL4512213</td>\n",
       "      <td>EGFR(EGFRMGB1) Takeda global kinase panel</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000179</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>pIC50</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>6.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15262</th>\n",
       "      <td>None</td>\n",
       "      <td>23116841</td>\n",
       "      <td>[{'comments': None, 'relation': None, 'result_...</td>\n",
       "      <td>CHEMBL4512787</td>\n",
       "      <td>EGFR(EGFRMGB1) Takeda global kinase panel</td>\n",
       "      <td>B</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>BAO_0000179</td>\n",
       "      <td>BAO_0000357</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Epidermal growth factor receptor erbB1</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>pIC50</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>6.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>8915 rows × 45 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      activity_comment  activity_id  \\\n",
       "0                 None        32260   \n",
       "3                 None        32267   \n",
       "6                 None        32680   \n",
       "7                 None        32770   \n",
       "8                 None        32772   \n",
       "...                ...          ...   \n",
       "15258       Not Active     23070040   \n",
       "15259             None     23090818   \n",
       "15260             None     23116071   \n",
       "15261             None     23116480   \n",
       "15262             None     23116841   \n",
       "\n",
       "                                     activity_properties assay_chembl_id  \\\n",
       "0                                                     []    CHEMBL674637   \n",
       "3                                                     []    CHEMBL674637   \n",
       "6                                                     []    CHEMBL677833   \n",
       "7                                                     []    CHEMBL674643   \n",
       "8                                                     []    CHEMBL674643   \n",
       "...                                                  ...             ...   \n",
       "15258  [{'comments': None, 'relation': None, 'result_...   CHEMBL4509084   \n",
       "15259                                                 []   CHEMBL4510669   \n",
       "15260  [{'comments': None, 'relation': None, 'result_...   CHEMBL4512500   \n",
       "15261  [{'comments': None, 'relation': None, 'result_...   CHEMBL4512213   \n",
       "15262  [{'comments': None, 'relation': None, 'result_...   CHEMBL4512787   \n",
       "\n",
       "                                       assay_description assay_type  \\\n",
       "0      Inhibitory activity towards tyrosine phosphory...          B   \n",
       "3      Inhibitory activity towards tyrosine phosphory...          B   \n",
       "6      In vitro inhibition of Epidermal growth factor...          B   \n",
       "7      Inhibitory concentration of EGF dependent auto...          B   \n",
       "8      Inhibitory concentration of EGF dependent auto...          B   \n",
       "...                                                  ...        ...   \n",
       "15258                       EGFR kinase inhibition assay          B   \n",
       "15259  Protein Tyrosine Kinase, EGF Receptor Eurofins...          B   \n",
       "15260          EGFR(EGFRMGB1) Takeda global kinase panel          B   \n",
       "15261          EGFR(EGFRMGB1) Takeda global kinase panel          B   \n",
       "15262          EGFR(EGFRMGB1) Takeda global kinase panel          B   \n",
       "\n",
       "      assay_variant_accession assay_variant_mutation bao_endpoint  \\\n",
       "0                        None                   None  BAO_0000190   \n",
       "3                        None                   None  BAO_0000190   \n",
       "6                        None                   None  BAO_0000190   \n",
       "7                        None                   None  BAO_0000190   \n",
       "8                        None                   None  BAO_0000190   \n",
       "...                       ...                    ...          ...   \n",
       "15258                    None                   None  BAO_0000179   \n",
       "15259                    None                   None  BAO_0000179   \n",
       "15260                    None                   None  BAO_0000179   \n",
       "15261                    None                   None  BAO_0000179   \n",
       "15262                    None                   None  BAO_0000179   \n",
       "\n",
       "        bao_format  ... target_organism  \\\n",
       "0      BAO_0000357  ...    Homo sapiens   \n",
       "3      BAO_0000357  ...    Homo sapiens   \n",
       "6      BAO_0000357  ...    Homo sapiens   \n",
       "7      BAO_0000357  ...    Homo sapiens   \n",
       "8      BAO_0000357  ...    Homo sapiens   \n",
       "...            ...  ...             ...   \n",
       "15258  BAO_0000357  ...    Homo sapiens   \n",
       "15259  BAO_0000357  ...    Homo sapiens   \n",
       "15260  BAO_0000357  ...    Homo sapiens   \n",
       "15261  BAO_0000357  ...    Homo sapiens   \n",
       "15262  BAO_0000357  ...    Homo sapiens   \n",
       "\n",
       "                             target_pref_name target_tax_id text_value  toid  \\\n",
       "0      Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "3      Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "6      Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "7      Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "8      Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "...                                       ...           ...        ...   ...   \n",
       "15258  Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "15259  Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "15260  Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "15261  Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "15262  Epidermal growth factor receptor erbB1          9606       None  None   \n",
       "\n",
       "        type  units    uo_units upper_value   value  \n",
       "0       IC50     uM  UO_0000065        None   0.041  \n",
       "3       IC50     uM  UO_0000065        None    0.17  \n",
       "6       IC50     uM  UO_0000065        None     9.3  \n",
       "7       IC50     uM  UO_0000065        None   500.0  \n",
       "8       IC50     uM  UO_0000065        None  3000.0  \n",
       "...      ...    ...         ...         ...     ...  \n",
       "15258   IC50     µM        None        None    20.0  \n",
       "15259   IC50     µM        None        None    4.59  \n",
       "15260  pIC50   None        None        None     6.0  \n",
       "15261  pIC50   None        None        None     6.0  \n",
       "15262  pIC50   None        None        None     6.0  \n",
       "\n",
       "[8915 rows x 45 columns]"
      ]
     },
     "execution_count": 51,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df2_nr = df2.drop_duplicates(['canonical_smiles'])\n",
    "df2_nr"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Data pre-processing of bioactivity data"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Combine the three columns (molecule_chembl_id, anonical_smiles, standard_value) and bioactivity_class into a DataFrame"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "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>molecule_chembl_id</th>\n",
       "      <th>canonical_smiles</th>\n",
       "      <th>standard_value</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>CHEMBL68920</td>\n",
       "      <td>Cc1cc(C)c(/C=C2\\C(=O)Nc3ncnc(Nc4ccc(F)c(Cl)c4)...</td>\n",
       "      <td>41.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>CHEMBL68920</td>\n",
       "      <td>Cc1cc(C)c(/C=C2\\C(=O)Nc3ncnc(Nc4ccc(F)c(Cl)c4)...</td>\n",
       "      <td>300.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>CHEMBL68920</td>\n",
       "      <td>Cc1cc(C)c(/C=C2\\C(=O)Nc3ncnc(Nc4ccc(F)c(Cl)c4)...</td>\n",
       "      <td>7820.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>CHEMBL69960</td>\n",
       "      <td>Cc1cc(C(=O)N2CCOCC2)[nH]c1/C=C1\\C(=O)Nc2ncnc(N...</td>\n",
       "      <td>170.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>CHEMBL69960</td>\n",
       "      <td>Cc1cc(C(=O)N2CCOCC2)[nH]c1/C=C1\\C(=O)Nc2ncnc(N...</td>\n",
       "      <td>40.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15258</th>\n",
       "      <td>CHEMBL4520788</td>\n",
       "      <td>CNCc1ccccc1-c1csc([C@H](C)Nc2nc(C)nc3cc(OC)c(O...</td>\n",
       "      <td>20.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15259</th>\n",
       "      <td>CHEMBL1800685</td>\n",
       "      <td>O=C(O)c1cc(-c2ccc(C3CCNCC3)cc2)c2ccc(-c3ccc(C(...</td>\n",
       "      <td>4.59</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15260</th>\n",
       "      <td>CHEMBL4088216</td>\n",
       "      <td>CN1C(=O)[C@@H](N2CCc3cn(Cc4ccccc4)nc3C2=O)COc2...</td>\n",
       "      <td>1000.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15261</th>\n",
       "      <td>CHEMBL4549667</td>\n",
       "      <td>CN1C(=O)[C@@H](N2CCc3c(nn(Cc4ccccc4)c3Br)C2=O)...</td>\n",
       "      <td>1000.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15262</th>\n",
       "      <td>CHEMBL4097778</td>\n",
       "      <td>CN1C(=O)[C@@H](N2CCc3cn(CC4CCS(=O)(=O)CC4)nc3C...</td>\n",
       "      <td>1000.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>13897 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      molecule_chembl_id                                   canonical_smiles  \\\n",
       "0            CHEMBL68920  Cc1cc(C)c(/C=C2\\C(=O)Nc3ncnc(Nc4ccc(F)c(Cl)c4)...   \n",
       "1            CHEMBL68920  Cc1cc(C)c(/C=C2\\C(=O)Nc3ncnc(Nc4ccc(F)c(Cl)c4)...   \n",
       "2            CHEMBL68920  Cc1cc(C)c(/C=C2\\C(=O)Nc3ncnc(Nc4ccc(F)c(Cl)c4)...   \n",
       "3            CHEMBL69960  Cc1cc(C(=O)N2CCOCC2)[nH]c1/C=C1\\C(=O)Nc2ncnc(N...   \n",
       "4            CHEMBL69960  Cc1cc(C(=O)N2CCOCC2)[nH]c1/C=C1\\C(=O)Nc2ncnc(N...   \n",
       "...                  ...                                                ...   \n",
       "15258      CHEMBL4520788  CNCc1ccccc1-c1csc([C@H](C)Nc2nc(C)nc3cc(OC)c(O...   \n",
       "15259      CHEMBL1800685  O=C(O)c1cc(-c2ccc(C3CCNCC3)cc2)c2ccc(-c3ccc(C(...   \n",
       "15260      CHEMBL4088216  CN1C(=O)[C@@H](N2CCc3cn(Cc4ccccc4)nc3C2=O)COc2...   \n",
       "15261      CHEMBL4549667  CN1C(=O)[C@@H](N2CCc3c(nn(Cc4ccccc4)c3Br)C2=O)...   \n",
       "15262      CHEMBL4097778  CN1C(=O)[C@@H](N2CCc3cn(CC4CCS(=O)(=O)CC4)nc3C...   \n",
       "\n",
       "      standard_value  \n",
       "0               41.0  \n",
       "1              300.0  \n",
       "2             7820.0  \n",
       "3              170.0  \n",
       "4               40.0  \n",
       "...              ...  \n",
       "15258           20.0  \n",
       "15259           4.59  \n",
       "15260         1000.0  \n",
       "15261         1000.0  \n",
       "15262         1000.0  \n",
       "\n",
       "[13897 rows x 3 columns]"
      ]
     },
     "execution_count": 52,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "selection = ['molecule_chembl_id','canonical_smiles','standard_value']\n",
    "df3 = df2[selection]\n",
    "df3"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 53,
   "metadata": {},
   "outputs": [],
   "source": [
    "# save dataframe to CSV file\n",
    "df3.to_csv('EGFR_02_bioactivity_data_preprocessed.csv', index=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Labeling compounds as active, inactive, or intermediate"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The IC50 unit contains the bioactivity data. Compounds are classified accourding to the following parameters:\n",
    "- Active:   IC50 <= 1,000 nM\n",
    "- Inactive: IC50 >= 10,000 nM \n",
    "- Values in between 1,000 and 10,000 nM will be considered as intermediate."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "metadata": {},
   "outputs": [],
   "source": [
    "df4 = pd.read_csv('EGFR_02_bioactivity_data_preprocessed.csv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 55,
   "metadata": {},
   "outputs": [],
   "source": [
    "bioactivity_threshold = []\n",
    "for i in df4.standard_value:\n",
    "  if float(i) >= 10000:\n",
    "    bioactivity_threshold.append(\"inactive\")\n",
    "  elif float(i) <= 1000:\n",
    "    bioactivity_threshold.append(\"active\")\n",
    "  else:\n",
    "    bioactivity_threshold.append(\"intermediate\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 56,
   "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>molecule_chembl_id</th>\n",
       "      <th>canonical_smiles</th>\n",
       "      <th>standard_value</th>\n",
       "      <th>class</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>CHEMBL68920</td>\n",
       "      <td>Cc1cc(C)c(/C=C2\\C(=O)Nc3ncnc(Nc4ccc(F)c(Cl)c4)...</td>\n",
       "      <td>41.00</td>\n",
       "      <td>active</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>CHEMBL68920</td>\n",
       "      <td>Cc1cc(C)c(/C=C2\\C(=O)Nc3ncnc(Nc4ccc(F)c(Cl)c4)...</td>\n",
       "      <td>300.00</td>\n",
       "      <td>active</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>CHEMBL68920</td>\n",
       "      <td>Cc1cc(C)c(/C=C2\\C(=O)Nc3ncnc(Nc4ccc(F)c(Cl)c4)...</td>\n",
       "      <td>7820.00</td>\n",
       "      <td>intermediate</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>CHEMBL69960</td>\n",
       "      <td>Cc1cc(C(=O)N2CCOCC2)[nH]c1/C=C1\\C(=O)Nc2ncnc(N...</td>\n",
       "      <td>170.00</td>\n",
       "      <td>active</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>CHEMBL69960</td>\n",
       "      <td>Cc1cc(C(=O)N2CCOCC2)[nH]c1/C=C1\\C(=O)Nc2ncnc(N...</td>\n",
       "      <td>40.00</td>\n",
       "      <td>active</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>13892</th>\n",
       "      <td>CHEMBL4520788</td>\n",
       "      <td>CNCc1ccccc1-c1csc([C@H](C)Nc2nc(C)nc3cc(OC)c(O...</td>\n",
       "      <td>20.00</td>\n",
       "      <td>active</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13893</th>\n",
       "      <td>CHEMBL1800685</td>\n",
       "      <td>O=C(O)c1cc(-c2ccc(C3CCNCC3)cc2)c2ccc(-c3ccc(C(...</td>\n",
       "      <td>4.59</td>\n",
       "      <td>active</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13894</th>\n",
       "      <td>CHEMBL4088216</td>\n",
       "      <td>CN1C(=O)[C@@H](N2CCc3cn(Cc4ccccc4)nc3C2=O)COc2...</td>\n",
       "      <td>1000.00</td>\n",
       "      <td>active</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13895</th>\n",
       "      <td>CHEMBL4549667</td>\n",
       "      <td>CN1C(=O)[C@@H](N2CCc3c(nn(Cc4ccccc4)c3Br)C2=O)...</td>\n",
       "      <td>1000.00</td>\n",
       "      <td>active</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13896</th>\n",
       "      <td>CHEMBL4097778</td>\n",
       "      <td>CN1C(=O)[C@@H](N2CCc3cn(CC4CCS(=O)(=O)CC4)nc3C...</td>\n",
       "      <td>1000.00</td>\n",
       "      <td>active</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>13897 rows × 4 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      molecule_chembl_id                                   canonical_smiles  \\\n",
       "0            CHEMBL68920  Cc1cc(C)c(/C=C2\\C(=O)Nc3ncnc(Nc4ccc(F)c(Cl)c4)...   \n",
       "1            CHEMBL68920  Cc1cc(C)c(/C=C2\\C(=O)Nc3ncnc(Nc4ccc(F)c(Cl)c4)...   \n",
       "2            CHEMBL68920  Cc1cc(C)c(/C=C2\\C(=O)Nc3ncnc(Nc4ccc(F)c(Cl)c4)...   \n",
       "3            CHEMBL69960  Cc1cc(C(=O)N2CCOCC2)[nH]c1/C=C1\\C(=O)Nc2ncnc(N...   \n",
       "4            CHEMBL69960  Cc1cc(C(=O)N2CCOCC2)[nH]c1/C=C1\\C(=O)Nc2ncnc(N...   \n",
       "...                  ...                                                ...   \n",
       "13892      CHEMBL4520788  CNCc1ccccc1-c1csc([C@H](C)Nc2nc(C)nc3cc(OC)c(O...   \n",
       "13893      CHEMBL1800685  O=C(O)c1cc(-c2ccc(C3CCNCC3)cc2)c2ccc(-c3ccc(C(...   \n",
       "13894      CHEMBL4088216  CN1C(=O)[C@@H](N2CCc3cn(Cc4ccccc4)nc3C2=O)COc2...   \n",
       "13895      CHEMBL4549667  CN1C(=O)[C@@H](N2CCc3c(nn(Cc4ccccc4)c3Br)C2=O)...   \n",
       "13896      CHEMBL4097778  CN1C(=O)[C@@H](N2CCc3cn(CC4CCS(=O)(=O)CC4)nc3C...   \n",
       "\n",
       "       standard_value         class  \n",
       "0               41.00        active  \n",
       "1              300.00        active  \n",
       "2             7820.00  intermediate  \n",
       "3              170.00        active  \n",
       "4               40.00        active  \n",
       "...               ...           ...  \n",
       "13892           20.00        active  \n",
       "13893            4.59        active  \n",
       "13894         1000.00        active  \n",
       "13895         1000.00        active  \n",
       "13896         1000.00        active  \n",
       "\n",
       "[13897 rows x 4 columns]"
      ]
     },
     "execution_count": 56,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# adds bioactivity class to the dataframe\n",
    "bioactivity_class = pd.Series(bioactivity_threshold, name='class')\n",
    "df5 = pd.concat([df4, bioactivity_class], axis=1)\n",
    "df5"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 57,
   "metadata": {},
   "outputs": [],
   "source": [
    "# save dataframe to CSV file\n",
    "df5.to_csv('EGFR_03_bioactivity_data_curated.csv', index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 58,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "updating: EGFR_01_bioactivity_data_raw.csv (deflated 92%)\n",
      "updating: EGFR_02_bioactivity_data_preprocessed.csv (deflated 85%)\n",
      "updating: EGFR_03_bioactivity_data_curated.csv (deflated 86%)\n",
      "updating: Pks13_bioactivity_data_2class_pIC50.csv (deflated 80%)\n",
      "updating: Pks13_bioactivity_data_3class_pIC50_pubchem_fp.csv (deflated 95%)\n",
      "updating: acetylcholinesterase_01_bioactivity_data_raw.csv (deflated 91%)\n",
      "updating: acetylcholinesterase_02_bioactivity_data_preprocessed.csv (deflated 82%)\n",
      "updating: acetylcholinesterase_03_bioactivity_data_curated.csv (deflated 83%)\n",
      "updating: acetylcholinesterase_04_bioactivity_data_3class_pIC50.csv (deflated 78%)\n",
      "updating: acetylcholinesterase_05_bioactivity_data_2class_pIC50.csv (deflated 78%)\n",
      "updating: bioactivity_data.csv (deflated 93%)\n",
      "updating: bioactivity_data_raw.csv (deflated 91%)\n",
      "updating: bioactivity_preprocessed_data.csv (deflated 85%)\n",
      "updating: descriptors_output.csv (deflated 95%)\n",
      "updating: mannwhitneyu_LogP.csv (deflated 9%)\n",
      "updating: mannwhitneyu_MW.csv (deflated 7%)\n",
      "updating: mannwhitneyu_NumHAcceptors.csv (deflated 10%)\n",
      "updating: mannwhitneyu_NumHDonors.csv (deflated 8%)\n",
      "updating: mannwhitneyu_pIC50.csv (deflated 11%)\n"
     ]
    }
   ],
   "source": [
    "! zip EGFR.zip *.csv"
   ]
  }
 ],
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