CDD_ML_Part_1_Acetylcholinesterase_Bioactivity_Data_Concised.ipynb

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  "metadata": {
    "colab": {
      "name": "CDD-ML-Part-1-Bioactivity-Data-Concised-Acetylcholinesterase.ipynb",
      "provenance": [],
      "collapsed_sections": []
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    }
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  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "wSFbIMb87cHu",
        "colab_type": "text"
      },
      "source": [
        "# **Bioinformatics Project - Computational Drug Discovery [Part 1] Download Bioactivity Data (Concised version)**\n",
        "\n",
        "Chanin Nantasenamat\n",
        "\n",
        "[*'Data Professor' YouTube channel*](http://youtube.com/dataprofessor)\n",
        "\n",
        "In this Jupyter notebook, we will be building a real-life **data science project** that you can include in your **data science portfolio**. Particularly, we will be building a machine learning model using the ChEMBL bioactivity data.\n",
        "\n",
        "In **Part 1**, we will be performing Data Collection and Pre-Processing from the ChEMBL Database.\n",
        "\n",
        "Note for this Concised Version:\n",
        "* Redundant code cells were deleted.\n",
        "* Code cells for saving files to Google Drive has been deleted.\n",
        "\n",
        "---"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "3iQiERxumDor",
        "colab_type": "text"
      },
      "source": [
        "## **ChEMBL Database**\n",
        "\n",
        "The [*ChEMBL Database*](https://www.ebi.ac.uk/chembl/) is a database that contains curated bioactivity data of more than 2 million compounds. It is compiled from more than 76,000 documents, 1.2 million assays and the data spans 13,000 targets and 1,800 cells and 33,000 indications.\n",
        "[Data as of March 25, 2020; ChEMBL version 26]."
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "iryGAwAIQ4yf",
        "colab_type": "text"
      },
      "source": [
        "## **Installing libraries**"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "toGT1U_B7F2i",
        "colab_type": "text"
      },
      "source": [
        "Install the ChEMBL web service package so that we can retrieve bioactivity data from the ChEMBL Database."
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "cJGExHQBfLh7",
        "colab_type": "code",
        "outputId": "dbeeb7ab-426b-481f-ca15-897f6c09451c",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 343
        }
      },
      "source": [
        "! pip install chembl_webresource_client"
      ],
      "execution_count": 0,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "Collecting chembl_webresource_client\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/2e/48/0db29040c92726fcc6f99a5bc89e0ea8cf5a9d84753ebaaf53108792da2a/chembl-webresource-client-0.10.2.tar.gz (51kB)\n",
            "\r\u001b[K     |██████▍                         | 10kB 21.5MB/s eta 0:00:01\r\u001b[K     |████████████▊                   | 20kB 1.7MB/s eta 0:00:01\r\u001b[K     |███████████████████             | 30kB 2.5MB/s eta 0:00:01\r\u001b[K     |█████████████████████████▍      | 40kB 3.3MB/s eta 0:00:01\r\u001b[K     |███████████████████████████████▊| 51kB 2.1MB/s eta 0:00:01\r\u001b[K     |████████████████████████████████| 61kB 2.1MB/s \n",
            "\u001b[?25hRequirement already satisfied: urllib3 in /usr/local/lib/python3.6/dist-packages (from chembl_webresource_client) (1.24.3)\n",
            "Requirement already satisfied: requests>=2.18.4 in /usr/local/lib/python3.6/dist-packages (from chembl_webresource_client) (2.23.0)\n",
            "Collecting requests-cache>=0.4.7\n",
            "  Downloading https://files.pythonhosted.org/packages/7f/55/9b1c40eb83c16d8fc79c5f6c2ffade04208b080670fbfc35e0a5effb5a92/requests_cache-0.5.2-py2.py3-none-any.whl\n",
            "Requirement already satisfied: easydict in /usr/local/lib/python3.6/dist-packages (from chembl_webresource_client) (1.9)\n",
            "Requirement already satisfied: idna<3,>=2.5 in /usr/local/lib/python3.6/dist-packages (from requests>=2.18.4->chembl_webresource_client) (2.9)\n",
            "Requirement already satisfied: chardet<4,>=3.0.2 in /usr/local/lib/python3.6/dist-packages (from requests>=2.18.4->chembl_webresource_client) (3.0.4)\n",
            "Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.6/dist-packages (from requests>=2.18.4->chembl_webresource_client) (2020.4.5.1)\n",
            "Building wheels for collected packages: chembl-webresource-client\n",
            "  Building wheel for chembl-webresource-client (setup.py) ... \u001b[?25l\u001b[?25hdone\n",
            "  Created wheel for chembl-webresource-client: filename=chembl_webresource_client-0.10.2-cp36-none-any.whl size=55661 sha256=a52d78c7928723755f476d68cdfcd640830e02a8ab2d24d68d28e0d0df1dcf8d\n",
            "  Stored in directory: /root/.cache/pip/wheels/e6/96/19/3f042bfda7c669bfe24c8278477f57b0fbbf3e488b4c09e3a8\n",
            "Successfully built chembl-webresource-client\n",
            "Installing collected packages: requests-cache, chembl-webresource-client\n",
            "Successfully installed chembl-webresource-client-0.10.2 requests-cache-0.5.2\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "J0kJjL8gb5nX",
        "colab_type": "text"
      },
      "source": [
        "## **Importing libraries**"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "RXoCvMPPfNrv",
        "colab_type": "code",
        "colab": {}
      },
      "source": [
        "# Import necessary libraries\n",
        "import pandas as pd\n",
        "from chembl_webresource_client.new_client import new_client"
      ],
      "execution_count": 0,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "1FgUai1bfigC",
        "colab_type": "text"
      },
      "source": [
        "## **Search for Target protein**"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "7lBsDrD0gAqH",
        "colab_type": "text"
      },
      "source": [
        "### **Target search for Acetylcholinesterase**"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "Vxtp79so4ZjF",
        "colab_type": "code",
        "outputId": "92e78250-8b71-4912-f0eb-dd48bb563aaa",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 1000
        }
      },
      "source": [
        "# Target search for coronavirus\n",
        "target = new_client.target\n",
        "target_query = target.search('acetylcholinesterase')\n",
        "targets = pd.DataFrame.from_dict(target_query)\n",
        "targets"
      ],
      "execution_count": 0,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
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              "  <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",
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              "      <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': 'P22303', 'xref_name': None, 'xre...</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</td>\n",
              "      <td>27.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>[{'accession': 'P22303', 'component_descriptio...</td>\n",
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              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>[]</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Cholinesterases; ACHE &amp; BCHE</td>\n",
              "      <td>27.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL2095233</td>\n",
              "      <td>[{'accession': 'P06276', 'component_descriptio...</td>\n",
              "      <td>SELECTIVITY GROUP</td>\n",
              "      <td>9606</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>[]</td>\n",
              "      <td>Drosophila melanogaster</td>\n",
              "      <td>Acetylcholinesterase</td>\n",
              "      <td>17.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL2242744</td>\n",
              "      <td>[{'accession': 'P07140', 'component_descriptio...</td>\n",
              "      <td>SINGLE PROTEIN</td>\n",
              "      <td>7227</td>\n",
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              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>[]</td>\n",
              "      <td>Nephotettix cincticeps</td>\n",
              "      <td>Ace-orthologous acetylcholinesterase</td>\n",
              "      <td>17.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL2366514</td>\n",
              "      <td>[{'accession': 'Q9NJH6', 'component_descriptio...</td>\n",
              "      <td>SINGLE PROTEIN</td>\n",
              "      <td>94400</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>[{'xref_id': 'P04058', 'xref_name': None, 'xre...</td>\n",
              "      <td>Torpedo californica</td>\n",
              "      <td>Acetylcholinesterase</td>\n",
              "      <td>15.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL4780</td>\n",
              "      <td>[{'accession': 'P04058', 'component_descriptio...</td>\n",
              "      <td>SINGLE PROTEIN</td>\n",
              "      <td>7787</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>5</th>\n",
              "      <td>[{'xref_id': 'P21836', 'xref_name': None, 'xre...</td>\n",
              "      <td>Mus musculus</td>\n",
              "      <td>Acetylcholinesterase</td>\n",
              "      <td>15.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL3198</td>\n",
              "      <td>[{'accession': 'P21836', 'component_descriptio...</td>\n",
              "      <td>SINGLE PROTEIN</td>\n",
              "      <td>10090</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>6</th>\n",
              "      <td>[{'xref_id': 'P37136', 'xref_name': None, 'xre...</td>\n",
              "      <td>Rattus norvegicus</td>\n",
              "      <td>Acetylcholinesterase</td>\n",
              "      <td>15.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL3199</td>\n",
              "      <td>[{'accession': 'P37136', 'component_descriptio...</td>\n",
              "      <td>SINGLE PROTEIN</td>\n",
              "      <td>10116</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7</th>\n",
              "      <td>[{'xref_id': 'O42275', 'xref_name': None, 'xre...</td>\n",
              "      <td>Electrophorus electricus</td>\n",
              "      <td>Acetylcholinesterase</td>\n",
              "      <td>15.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL4078</td>\n",
              "      <td>[{'accession': 'O42275', 'component_descriptio...</td>\n",
              "      <td>SINGLE PROTEIN</td>\n",
              "      <td>8005</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>8</th>\n",
              "      <td>[{'xref_id': 'P23795', 'xref_name': None, 'xre...</td>\n",
              "      <td>Bos taurus</td>\n",
              "      <td>Acetylcholinesterase</td>\n",
              "      <td>15.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL4768</td>\n",
              "      <td>[{'accession': 'P23795', 'component_descriptio...</td>\n",
              "      <td>SINGLE PROTEIN</td>\n",
              "      <td>9913</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>9</th>\n",
              "      <td>[]</td>\n",
              "      <td>Anopheles gambiae</td>\n",
              "      <td>Acetylcholinesterase</td>\n",
              "      <td>15.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL2046266</td>\n",
              "      <td>[{'accession': 'Q869C3', 'component_descriptio...</td>\n",
              "      <td>SINGLE PROTEIN</td>\n",
              "      <td>7165</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>10</th>\n",
              "      <td>[]</td>\n",
              "      <td>Leptinotarsa decemlineata</td>\n",
              "      <td>Acetylcholinesterase</td>\n",
              "      <td>15.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL2366490</td>\n",
              "      <td>[{'accession': 'Q27677', 'component_descriptio...</td>\n",
              "      <td>SINGLE PROTEIN</td>\n",
              "      <td>7539</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>11</th>\n",
              "      <td>[]</td>\n",
              "      <td>Gallus gallus</td>\n",
              "      <td>Acetylcholinesterase</td>\n",
              "      <td>15.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL3227914</td>\n",
              "      <td>[{'accession': 'P36196', 'component_descriptio...</td>\n",
              "      <td>SINGLE PROTEIN</td>\n",
              "      <td>9031</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>12</th>\n",
              "      <td>[]</td>\n",
              "      <td>Danio rerio</td>\n",
              "      <td>Acetylcholinesterase</td>\n",
              "      <td>15.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL3308995</td>\n",
              "      <td>[{'accession': 'Q9DDE3', 'component_descriptio...</td>\n",
              "      <td>SINGLE PROTEIN</td>\n",
              "      <td>7955</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>13</th>\n",
              "      <td>[]</td>\n",
              "      <td>Aedes aegypti</td>\n",
              "      <td>Acetylcholinesterase</td>\n",
              "      <td>15.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL4295607</td>\n",
              "      <td>[{'accession': 'Q6A2E2', 'component_descriptio...</td>\n",
              "      <td>SINGLE PROTEIN</td>\n",
              "      <td>7159</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>14</th>\n",
              "      <td>[{'xref_id': 'Q95P20', 'xref_name': None, 'xre...</td>\n",
              "      <td>Musca domestica</td>\n",
              "      <td>Acetylcholinesterase</td>\n",
              "      <td>14.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL5752</td>\n",
              "      <td>[{'accession': 'Q95P20', 'component_descriptio...</td>\n",
              "      <td>SINGLE PROTEIN</td>\n",
              "      <td>7370</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>15</th>\n",
              "      <td>[]</td>\n",
              "      <td>Plutella xylostella</td>\n",
              "      <td>Acetylcholinesterase</td>\n",
              "      <td>14.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL2242729</td>\n",
              "      <td>[{'accession': 'Q8MZM0', 'component_descriptio...</td>\n",
              "      <td>SINGLE PROTEIN</td>\n",
              "      <td>51655</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>16</th>\n",
              "      <td>[]</td>\n",
              "      <td>Musca domestica</td>\n",
              "      <td>Acetylcholinesterase</td>\n",
              "      <td>14.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL2242743</td>\n",
              "      <td>[{'accession': 'Q7YWJ9', 'component_descriptio...</td>\n",
              "      <td>SINGLE PROTEIN</td>\n",
              "      <td>7370</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>17</th>\n",
              "      <td>[]</td>\n",
              "      <td>Pediculus humanus capitis</td>\n",
              "      <td>Acetylcholinesterase</td>\n",
              "      <td>14.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL2362988</td>\n",
              "      <td>[{'accession': 'A2PZ98', 'component_descriptio...</td>\n",
              "      <td>SINGLE PROTEIN</td>\n",
              "      <td>121226</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>18</th>\n",
              "      <td>[]</td>\n",
              "      <td>Spodoptera litura</td>\n",
              "      <td>Acetylcholinesterase</td>\n",
              "      <td>14.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL2366422</td>\n",
              "      <td>[{'accession': 'C5IU80', 'component_descriptio...</td>\n",
              "      <td>SINGLE PROTEIN</td>\n",
              "      <td>69820</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>19</th>\n",
              "      <td>[]</td>\n",
              "      <td>Laodelphax striatella</td>\n",
              "      <td>Acetylcholinesterase</td>\n",
              "      <td>14.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL2366446</td>\n",
              "      <td>[{'accession': 'K4JQ36', 'component_descriptio...</td>\n",
              "      <td>SINGLE PROTEIN</td>\n",
              "      <td>195883</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>20</th>\n",
              "      <td>[]</td>\n",
              "      <td>Schizaphis graminum</td>\n",
              "      <td>Acetylcholinesterase</td>\n",
              "      <td>14.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL2366511</td>\n",
              "      <td>[{'accession': 'Q9BMJ1', 'component_descriptio...</td>\n",
              "      <td>SINGLE PROTEIN</td>\n",
              "      <td>13262</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>21</th>\n",
              "      <td>[]</td>\n",
              "      <td>Caenorhabditis elegans</td>\n",
              "      <td>Acetylcholinesterase 1</td>\n",
              "      <td>14.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL3341583</td>\n",
              "      <td>[{'accession': 'P38433', 'component_descriptio...</td>\n",
              "      <td>SINGLE PROTEIN</td>\n",
              "      <td>6239</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>22</th>\n",
              "      <td>[]</td>\n",
              "      <td>Rattus norvegicus</td>\n",
              "      <td>Acetylcholinesterase and butyrylcholinesterase...</td>\n",
              "      <td>13.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL2111475</td>\n",
              "      <td>[{'accession': 'P37136', 'component_descriptio...</td>\n",
              "      <td>SELECTIVITY GROUP</td>\n",
              "      <td>10116</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "</div>"
            ],
            "text/plain": [
              "                                     cross_references  ...  tax_id\n",
              "0   [{'xref_id': 'P22303', 'xref_name': None, 'xre...  ...    9606\n",
              "1                                                  []  ...    9606\n",
              "2                                                  []  ...    7227\n",
              "3                                                  []  ...   94400\n",
              "4   [{'xref_id': 'P04058', 'xref_name': None, 'xre...  ...    7787\n",
              "5   [{'xref_id': 'P21836', 'xref_name': None, 'xre...  ...   10090\n",
              "6   [{'xref_id': 'P37136', 'xref_name': None, 'xre...  ...   10116\n",
              "7   [{'xref_id': 'O42275', 'xref_name': None, 'xre...  ...    8005\n",
              "8   [{'xref_id': 'P23795', 'xref_name': None, 'xre...  ...    9913\n",
              "9                                                  []  ...    7165\n",
              "10                                                 []  ...    7539\n",
              "11                                                 []  ...    9031\n",
              "12                                                 []  ...    7955\n",
              "13                                                 []  ...    7159\n",
              "14  [{'xref_id': 'Q95P20', 'xref_name': None, 'xre...  ...    7370\n",
              "15                                                 []  ...   51655\n",
              "16                                                 []  ...    7370\n",
              "17                                                 []  ...  121226\n",
              "18                                                 []  ...   69820\n",
              "19                                                 []  ...  195883\n",
              "20                                                 []  ...   13262\n",
              "21                                                 []  ...    6239\n",
              "22                                                 []  ...   10116\n",
              "\n",
              "[23 rows x 9 columns]"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 3
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "Y5OPfEALjAfZ",
        "colab_type": "text"
      },
      "source": [
        "### **Select and retrieve bioactivity data for *Human Acetylcholinesterase* (first entry)**"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "gSQ3aroOgML7",
        "colab_type": "text"
      },
      "source": [
        "We will assign the fifth entry (which corresponds to the target protein, *Human Acetylcholinesterase*) to the ***selected_target*** variable "
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "StrcHMVLha7u",
        "colab_type": "code",
        "outputId": "6cd12d1e-46b2-47ce-efcb-7d3c49fa3712",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 34
        }
      },
      "source": [
        "selected_target = targets.target_chembl_id[0]\n",
        "selected_target"
      ],
      "execution_count": 0,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "'CHEMBL220'"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 4
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "GWd2DRalgjzB",
        "colab_type": "text"
      },
      "source": [
        "Here, we will retrieve only bioactivity data for *Human Acetylcholinesterase* (CHEMBL220) that are reported as pChEMBL values."
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "LeFbV_CsSP8D",
        "colab_type": "code",
        "colab": {}
      },
      "source": [
        "activity = new_client.activity\n",
        "res = activity.filter(target_chembl_id=selected_target).filter(standard_type=\"IC50\")"
      ],
      "execution_count": 0,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "LrzAcEFnYzBY",
        "colab_type": "code",
        "colab": {}
      },
      "source": [
        "df = pd.DataFrame.from_dict(res)"
      ],
      "execution_count": 0,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "s9iUAXFdSkoM",
        "colab_type": "code",
        "outputId": "bb88ea44-9a54-44bf-b178-07558a80edb6",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 779
        }
      },
      "source": [
        "df"
      ],
      "execution_count": 0,
      "outputs": [
        {
          "output_type": "execute_result",
          "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>bao_endpoint</th>\n",
              "      <th>bao_format</th>\n",
              "      <th>bao_label</th>\n",
              "      <th>canonical_smiles</th>\n",
              "      <th>data_validity_comment</th>\n",
              "      <th>data_validity_description</th>\n",
              "      <th>document_chembl_id</th>\n",
              "      <th>document_journal</th>\n",
              "      <th>document_year</th>\n",
              "      <th>ligand_efficiency</th>\n",
              "      <th>molecule_chembl_id</th>\n",
              "      <th>molecule_pref_name</th>\n",
              "      <th>parent_molecule_chembl_id</th>\n",
              "      <th>pchembl_value</th>\n",
              "      <th>potential_duplicate</th>\n",
              "      <th>qudt_units</th>\n",
              "      <th>record_id</th>\n",
              "      <th>relation</th>\n",
              "      <th>src_id</th>\n",
              "      <th>standard_flag</th>\n",
              "      <th>standard_relation</th>\n",
              "      <th>standard_text_value</th>\n",
              "      <th>standard_type</th>\n",
              "      <th>standard_units</th>\n",
              "      <th>standard_upper_value</th>\n",
              "      <th>standard_value</th>\n",
              "      <th>target_chembl_id</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>33969</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL643384</td>\n",
              "      <td>Inhibitory concentration against acetylcholine...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>CCOc1nn(-c2cccc(OCc3ccccc3)c2)c(=O)o1</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>{'bei': '19.61', 'le': '0.36', 'lle': '3.32', ...</td>\n",
              "      <td>CHEMBL133897</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL133897</td>\n",
              "      <td>6.12</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252547</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>750.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>0.75</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>None</td>\n",
              "      <td>37563</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL643384</td>\n",
              "      <td>Inhibitory concentration against acetylcholine...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC1CC1</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>{'bei': '18.57', 'le': '0.38', 'lle': '2.45', ...</td>\n",
              "      <td>CHEMBL336398</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL336398</td>\n",
              "      <td>7.00</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252533</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>100.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>0.1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>None</td>\n",
              "      <td>37565</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL643384</td>\n",
              "      <td>Inhibitory concentration against acetylcholine...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>CN(C(=O)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F)c1ccccc1</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL131588</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL131588</td>\n",
              "      <td>None</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252530</td>\n",
              "      <td>&gt;</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>&gt;</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>50000.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>50.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>None</td>\n",
              "      <td>38902</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL643384</td>\n",
              "      <td>Inhibitory concentration against acetylcholine...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>{'bei': '16.11', 'le': '0.34', 'lle': '1.81', ...</td>\n",
              "      <td>CHEMBL130628</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL130628</td>\n",
              "      <td>6.52</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252534</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>300.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>4</th>\n",
              "      <td>None</td>\n",
              "      <td>41170</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL643384</td>\n",
              "      <td>Inhibitory concentration against acetylcholine...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>CSc1nc(-c2ccc(OC(F)(F)F)cc2)nn1C(=O)N(C)C</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>{'bei': '17.60', 'le': '0.36', 'lle': '3.00', ...</td>\n",
              "      <td>CHEMBL130478</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL130478</td>\n",
              "      <td>6.10</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252552</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>800.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>0.8</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",
              "      <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",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7021</th>\n",
              "      <td>None</td>\n",
              "      <td>18798886</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4274263</td>\n",
              "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(Br)cc3)...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4270597</td>\n",
              "      <td>Eur J Med Chem</td>\n",
              "      <td>2018.0</td>\n",
              "      <td>{'bei': '9.75', 'le': '0.21', 'lle': '-1.76', ...</td>\n",
              "      <td>CHEMBL4281727</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4281727</td>\n",
              "      <td>5.42</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3124025</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>3810.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>3.81</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7022</th>\n",
              "      <td>None</td>\n",
              "      <td>18798887</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4274263</td>\n",
              "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3cccc([N+](=...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4270597</td>\n",
              "      <td>Eur J Med Chem</td>\n",
              "      <td>2018.0</td>\n",
              "      <td>{'bei': '10.47', 'le': '0.20', 'lle': '-0.87',...</td>\n",
              "      <td>CHEMBL4292349</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4292349</td>\n",
              "      <td>5.46</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3124026</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>3460.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>3.46</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7023</th>\n",
              "      <td>None</td>\n",
              "      <td>18798888</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4274263</td>\n",
              "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(C#N)cc3...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4270597</td>\n",
              "      <td>Eur J Med Chem</td>\n",
              "      <td>2018.0</td>\n",
              "      <td>{'bei': '11.07', 'le': '0.21', 'lle': '-0.73',...</td>\n",
              "      <td>CHEMBL4278260</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4278260</td>\n",
              "      <td>5.56</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3124027</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>2780.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>2.78</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7024</th>\n",
              "      <td>None</td>\n",
              "      <td>18798889</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4274263</td>\n",
              "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>O=C(/C=C/c1ccccc1)NCCC1CCN(Cc2ccccc2)CC1</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4270597</td>\n",
              "      <td>Eur J Med Chem</td>\n",
              "      <td>2018.0</td>\n",
              "      <td>{'bei': '18.21', 'le': '0.33', 'lle': '2.23', ...</td>\n",
              "      <td>CHEMBL3819548</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL3819548</td>\n",
              "      <td>6.35</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3124014</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>450.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>0.45</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7025</th>\n",
              "      <td>None</td>\n",
              "      <td>18798890</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4274263</td>\n",
              "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>O=C(/C=C/c1ccc(O)cc1)NCCC1CCN(Cc2ccccc2)CC1</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4270597</td>\n",
              "      <td>Eur J Med Chem</td>\n",
              "      <td>2018.0</td>\n",
              "      <td>{'bei': '15.36', 'le': '0.28', 'lle': '1.78', ...</td>\n",
              "      <td>CHEMBL3819320</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL3819320</td>\n",
              "      <td>5.60</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3124015</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>2510.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>2.51</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>7026 rows × 43 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "     activity_comment  activity_id  ... upper_value value\n",
              "0                None        33969  ...        None  0.75\n",
              "1                None        37563  ...        None   0.1\n",
              "2                None        37565  ...        None  50.0\n",
              "3                None        38902  ...        None   0.3\n",
              "4                None        41170  ...        None   0.8\n",
              "...               ...          ...  ...         ...   ...\n",
              "7021             None     18798886  ...        None  3.81\n",
              "7022             None     18798887  ...        None  3.46\n",
              "7023             None     18798888  ...        None  2.78\n",
              "7024             None     18798889  ...        None  0.45\n",
              "7025             None     18798890  ...        None  2.51\n",
              "\n",
              "[7026 rows x 43 columns]"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 7
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "fQ78N26Fg15T",
        "colab_type": "text"
      },
      "source": [
        "Finally we will save the resulting bioactivity data to a CSV file **bioactivity_data.csv**."
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "ZvUUEIVxTOH1",
        "colab_type": "code",
        "colab": {}
      },
      "source": [
        "df.to_csv('acetylcholinesterase_01_bioactivity_data_raw.csv', index=False)"
      ],
      "execution_count": 0,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "_GXMpFNUOn_8",
        "colab_type": "text"
      },
      "source": [
        "## **Handling missing data**\n",
        "If any compounds has missing value for the **standard_value** and **canonical_smiles** column then drop it."
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "hkVOdk6ZR396",
        "colab_type": "code",
        "outputId": "f8a638fe-75d1-4fae-d4c8-b3b1e6458174",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 813
        }
      },
      "source": [
        "df2 = df[df.standard_value.notna()]\n",
        "df2 = df2[df.canonical_smiles.notna()]\n",
        "df2"
      ],
      "execution_count": 0,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "/usr/local/lib/python3.6/dist-packages/ipykernel_launcher.py:2: UserWarning: Boolean Series key will be reindexed to match DataFrame index.\n",
            "  \n"
          ],
          "name": "stderr"
        },
        {
          "output_type": "execute_result",
          "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>bao_endpoint</th>\n",
              "      <th>bao_format</th>\n",
              "      <th>bao_label</th>\n",
              "      <th>canonical_smiles</th>\n",
              "      <th>data_validity_comment</th>\n",
              "      <th>data_validity_description</th>\n",
              "      <th>document_chembl_id</th>\n",
              "      <th>document_journal</th>\n",
              "      <th>document_year</th>\n",
              "      <th>ligand_efficiency</th>\n",
              "      <th>molecule_chembl_id</th>\n",
              "      <th>molecule_pref_name</th>\n",
              "      <th>parent_molecule_chembl_id</th>\n",
              "      <th>pchembl_value</th>\n",
              "      <th>potential_duplicate</th>\n",
              "      <th>qudt_units</th>\n",
              "      <th>record_id</th>\n",
              "      <th>relation</th>\n",
              "      <th>src_id</th>\n",
              "      <th>standard_flag</th>\n",
              "      <th>standard_relation</th>\n",
              "      <th>standard_text_value</th>\n",
              "      <th>standard_type</th>\n",
              "      <th>standard_units</th>\n",
              "      <th>standard_upper_value</th>\n",
              "      <th>standard_value</th>\n",
              "      <th>target_chembl_id</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>33969</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL643384</td>\n",
              "      <td>Inhibitory concentration against acetylcholine...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>CCOc1nn(-c2cccc(OCc3ccccc3)c2)c(=O)o1</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>{'bei': '19.61', 'le': '0.36', 'lle': '3.32', ...</td>\n",
              "      <td>CHEMBL133897</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL133897</td>\n",
              "      <td>6.12</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252547</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>750.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>0.75</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>None</td>\n",
              "      <td>37563</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL643384</td>\n",
              "      <td>Inhibitory concentration against acetylcholine...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC1CC1</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>{'bei': '18.57', 'le': '0.38', 'lle': '2.45', ...</td>\n",
              "      <td>CHEMBL336398</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL336398</td>\n",
              "      <td>7.00</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252533</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>100.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>0.1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>None</td>\n",
              "      <td>37565</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL643384</td>\n",
              "      <td>Inhibitory concentration against acetylcholine...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>CN(C(=O)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F)c1ccccc1</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL131588</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL131588</td>\n",
              "      <td>None</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252530</td>\n",
              "      <td>&gt;</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>&gt;</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>50000.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>50.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>None</td>\n",
              "      <td>38902</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL643384</td>\n",
              "      <td>Inhibitory concentration against acetylcholine...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>{'bei': '16.11', 'le': '0.34', 'lle': '1.81', ...</td>\n",
              "      <td>CHEMBL130628</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL130628</td>\n",
              "      <td>6.52</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252534</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>300.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>4</th>\n",
              "      <td>None</td>\n",
              "      <td>41170</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL643384</td>\n",
              "      <td>Inhibitory concentration against acetylcholine...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>CSc1nc(-c2ccc(OC(F)(F)F)cc2)nn1C(=O)N(C)C</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>{'bei': '17.60', 'le': '0.36', 'lle': '3.00', ...</td>\n",
              "      <td>CHEMBL130478</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL130478</td>\n",
              "      <td>6.10</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252552</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>800.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>0.8</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",
              "      <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",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7021</th>\n",
              "      <td>None</td>\n",
              "      <td>18798886</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4274263</td>\n",
              "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(Br)cc3)...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4270597</td>\n",
              "      <td>Eur J Med Chem</td>\n",
              "      <td>2018.0</td>\n",
              "      <td>{'bei': '9.75', 'le': '0.21', 'lle': '-1.76', ...</td>\n",
              "      <td>CHEMBL4281727</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4281727</td>\n",
              "      <td>5.42</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3124025</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>3810.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>3.81</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7022</th>\n",
              "      <td>None</td>\n",
              "      <td>18798887</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4274263</td>\n",
              "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3cccc([N+](=...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4270597</td>\n",
              "      <td>Eur J Med Chem</td>\n",
              "      <td>2018.0</td>\n",
              "      <td>{'bei': '10.47', 'le': '0.20', 'lle': '-0.87',...</td>\n",
              "      <td>CHEMBL4292349</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4292349</td>\n",
              "      <td>5.46</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3124026</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>3460.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>3.46</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7023</th>\n",
              "      <td>None</td>\n",
              "      <td>18798888</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4274263</td>\n",
              "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(C#N)cc3...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4270597</td>\n",
              "      <td>Eur J Med Chem</td>\n",
              "      <td>2018.0</td>\n",
              "      <td>{'bei': '11.07', 'le': '0.21', 'lle': '-0.73',...</td>\n",
              "      <td>CHEMBL4278260</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4278260</td>\n",
              "      <td>5.56</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3124027</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>2780.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>2.78</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7024</th>\n",
              "      <td>None</td>\n",
              "      <td>18798889</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4274263</td>\n",
              "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>O=C(/C=C/c1ccccc1)NCCC1CCN(Cc2ccccc2)CC1</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4270597</td>\n",
              "      <td>Eur J Med Chem</td>\n",
              "      <td>2018.0</td>\n",
              "      <td>{'bei': '18.21', 'le': '0.33', 'lle': '2.23', ...</td>\n",
              "      <td>CHEMBL3819548</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL3819548</td>\n",
              "      <td>6.35</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3124014</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>450.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>0.45</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7025</th>\n",
              "      <td>None</td>\n",
              "      <td>18798890</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4274263</td>\n",
              "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>O=C(/C=C/c1ccc(O)cc1)NCCC1CCN(Cc2ccccc2)CC1</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4270597</td>\n",
              "      <td>Eur J Med Chem</td>\n",
              "      <td>2018.0</td>\n",
              "      <td>{'bei': '15.36', 'le': '0.28', 'lle': '1.78', ...</td>\n",
              "      <td>CHEMBL3819320</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL3819320</td>\n",
              "      <td>5.60</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3124015</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>2510.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>2.51</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>5835 rows × 43 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "     activity_comment  activity_id  ... upper_value value\n",
              "0                None        33969  ...        None  0.75\n",
              "1                None        37563  ...        None   0.1\n",
              "2                None        37565  ...        None  50.0\n",
              "3                None        38902  ...        None   0.3\n",
              "4                None        41170  ...        None   0.8\n",
              "...               ...          ...  ...         ...   ...\n",
              "7021             None     18798886  ...        None  3.81\n",
              "7022             None     18798887  ...        None  3.46\n",
              "7023             None     18798888  ...        None  2.78\n",
              "7024             None     18798889  ...        None  0.45\n",
              "7025             None     18798890  ...        None  2.51\n",
              "\n",
              "[5835 rows x 43 columns]"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 9
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "wCkuaeVNbdtM",
        "colab_type": "code",
        "outputId": "9da80bc3-c1cb-4348-ce04-f90f57217995",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 34
        }
      },
      "source": [
        "len(df2.canonical_smiles.unique())"
      ],
      "execution_count": 0,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "4695"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 10
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "JbAK3K7wclkS",
        "colab_type": "code",
        "outputId": "1c623da3-bb53-44e8-8704-24161fa54d74",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 779
        }
      },
      "source": [
        "df2_nr = df2.drop_duplicates(['canonical_smiles'])\n",
        "df2_nr"
      ],
      "execution_count": 0,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/html": [
              "<div>\n",
              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
              "        vertical-align: middle;\n",
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              "\n",
              "    .dataframe tbody tr th {\n",
              "        vertical-align: top;\n",
              "    }\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>bao_endpoint</th>\n",
              "      <th>bao_format</th>\n",
              "      <th>bao_label</th>\n",
              "      <th>canonical_smiles</th>\n",
              "      <th>data_validity_comment</th>\n",
              "      <th>data_validity_description</th>\n",
              "      <th>document_chembl_id</th>\n",
              "      <th>document_journal</th>\n",
              "      <th>document_year</th>\n",
              "      <th>ligand_efficiency</th>\n",
              "      <th>molecule_chembl_id</th>\n",
              "      <th>molecule_pref_name</th>\n",
              "      <th>parent_molecule_chembl_id</th>\n",
              "      <th>pchembl_value</th>\n",
              "      <th>potential_duplicate</th>\n",
              "      <th>qudt_units</th>\n",
              "      <th>record_id</th>\n",
              "      <th>relation</th>\n",
              "      <th>src_id</th>\n",
              "      <th>standard_flag</th>\n",
              "      <th>standard_relation</th>\n",
              "      <th>standard_text_value</th>\n",
              "      <th>standard_type</th>\n",
              "      <th>standard_units</th>\n",
              "      <th>standard_upper_value</th>\n",
              "      <th>standard_value</th>\n",
              "      <th>target_chembl_id</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>33969</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL643384</td>\n",
              "      <td>Inhibitory concentration against acetylcholine...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>CCOc1nn(-c2cccc(OCc3ccccc3)c2)c(=O)o1</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>{'bei': '19.61', 'le': '0.36', 'lle': '3.32', ...</td>\n",
              "      <td>CHEMBL133897</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL133897</td>\n",
              "      <td>6.12</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252547</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>750.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>0.75</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>None</td>\n",
              "      <td>37563</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL643384</td>\n",
              "      <td>Inhibitory concentration against acetylcholine...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC1CC1</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>{'bei': '18.57', 'le': '0.38', 'lle': '2.45', ...</td>\n",
              "      <td>CHEMBL336398</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL336398</td>\n",
              "      <td>7.00</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252533</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>100.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>0.1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>None</td>\n",
              "      <td>37565</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL643384</td>\n",
              "      <td>Inhibitory concentration against acetylcholine...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>CN(C(=O)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F)c1ccccc1</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL131588</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL131588</td>\n",
              "      <td>None</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252530</td>\n",
              "      <td>&gt;</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>&gt;</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>50000.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>50.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>None</td>\n",
              "      <td>38902</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL643384</td>\n",
              "      <td>Inhibitory concentration against acetylcholine...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>{'bei': '16.11', 'le': '0.34', 'lle': '1.81', ...</td>\n",
              "      <td>CHEMBL130628</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL130628</td>\n",
              "      <td>6.52</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252534</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>300.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>4</th>\n",
              "      <td>None</td>\n",
              "      <td>41170</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL643384</td>\n",
              "      <td>Inhibitory concentration against acetylcholine...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>CSc1nc(-c2ccc(OC(F)(F)F)cc2)nn1C(=O)N(C)C</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1148382</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2004.0</td>\n",
              "      <td>{'bei': '17.60', 'le': '0.36', 'lle': '3.00', ...</td>\n",
              "      <td>CHEMBL130478</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL130478</td>\n",
              "      <td>6.10</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>252552</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>800.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>0.8</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",
              "      <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",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7019</th>\n",
              "      <td>None</td>\n",
              "      <td>18798884</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4274263</td>\n",
              "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccccc3Cl)CC...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4270597</td>\n",
              "      <td>Eur J Med Chem</td>\n",
              "      <td>2018.0</td>\n",
              "      <td>{'bei': '10.98', 'le': '0.21', 'lle': '-1.46',...</td>\n",
              "      <td>CHEMBL4293155</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4293155</td>\n",
              "      <td>5.61</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3124023</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>2440.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>2.44</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7020</th>\n",
              "      <td>None</td>\n",
              "      <td>18798885</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4274263</td>\n",
              "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3cccc(Cl)c3)...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4270597</td>\n",
              "      <td>Eur J Med Chem</td>\n",
              "      <td>2018.0</td>\n",
              "      <td>{'bei': '10.95', 'le': '0.21', 'lle': '-1.47',...</td>\n",
              "      <td>CHEMBL4282558</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4282558</td>\n",
              "      <td>5.59</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3124024</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>2540.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>2.54</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7021</th>\n",
              "      <td>None</td>\n",
              "      <td>18798886</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4274263</td>\n",
              "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(Br)cc3)...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4270597</td>\n",
              "      <td>Eur J Med Chem</td>\n",
              "      <td>2018.0</td>\n",
              "      <td>{'bei': '9.75', 'le': '0.21', 'lle': '-1.76', ...</td>\n",
              "      <td>CHEMBL4281727</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4281727</td>\n",
              "      <td>5.42</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3124025</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>3810.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>3.81</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7022</th>\n",
              "      <td>None</td>\n",
              "      <td>18798887</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4274263</td>\n",
              "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3cccc([N+](=...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4270597</td>\n",
              "      <td>Eur J Med Chem</td>\n",
              "      <td>2018.0</td>\n",
              "      <td>{'bei': '10.47', 'le': '0.20', 'lle': '-0.87',...</td>\n",
              "      <td>CHEMBL4292349</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4292349</td>\n",
              "      <td>5.46</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3124026</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>3460.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>3.46</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7023</th>\n",
              "      <td>None</td>\n",
              "      <td>18798888</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4274263</td>\n",
              "      <td>Inhibition of human erythrocyte AChE using ace...</td>\n",
              "      <td>B</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(C#N)cc3...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4270597</td>\n",
              "      <td>Eur J Med Chem</td>\n",
              "      <td>2018.0</td>\n",
              "      <td>{'bei': '11.07', 'le': '0.21', 'lle': '-0.73',...</td>\n",
              "      <td>CHEMBL4278260</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4278260</td>\n",
              "      <td>5.56</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3124027</td>\n",
              "      <td>=</td>\n",
              "      <td>1</td>\n",
              "      <td>True</td>\n",
              "      <td>=</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>2780.0</td>\n",
              "      <td>CHEMBL220</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Acetylcholinesterase</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>2.78</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>4695 rows × 43 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "     activity_comment  activity_id  ... upper_value value\n",
              "0                None        33969  ...        None  0.75\n",
              "1                None        37563  ...        None   0.1\n",
              "2                None        37565  ...        None  50.0\n",
              "3                None        38902  ...        None   0.3\n",
              "4                None        41170  ...        None   0.8\n",
              "...               ...          ...  ...         ...   ...\n",
              "7019             None     18798884  ...        None  2.44\n",
              "7020             None     18798885  ...        None  2.54\n",
              "7021             None     18798886  ...        None  3.81\n",
              "7022             None     18798887  ...        None  3.46\n",
              "7023             None     18798888  ...        None  2.78\n",
              "\n",
              "[4695 rows x 43 columns]"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 11
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "5H4sSFAWhV9B",
        "colab_type": "text"
      },
      "source": [
        "## **Data pre-processing of the bioactivity data**"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "Nv2dzid_hzKd",
        "colab_type": "text"
      },
      "source": [
        "### **Combine the 3 columns (molecule_chembl_id,canonical_smiles,standard_value) and bioactivity_class into a DataFrame**"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "0NCLYmrASgha",
        "colab_type": "code",
        "outputId": "d85ee5a6-e7bc-4be6-a621-6df526d065f9",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 419
        }
      },
      "source": [
        "selection = ['molecule_chembl_id','canonical_smiles','standard_value']\n",
        "df3 = df2_nr[selection]\n",
        "df3"
      ],
      "execution_count": 0,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
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              "<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>CHEMBL133897</td>\n",
              "      <td>CCOc1nn(-c2cccc(OCc3ccccc3)c2)c(=O)o1</td>\n",
              "      <td>750.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>CHEMBL336398</td>\n",
              "      <td>O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC1CC1</td>\n",
              "      <td>100.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>CHEMBL131588</td>\n",
              "      <td>CN(C(=O)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F)c1ccccc1</td>\n",
              "      <td>50000.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>CHEMBL130628</td>\n",
              "      <td>O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F</td>\n",
              "      <td>300.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>CHEMBL130478</td>\n",
              "      <td>CSc1nc(-c2ccc(OC(F)(F)F)cc2)nn1C(=O)N(C)C</td>\n",
              "      <td>800.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>...</th>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7019</th>\n",
              "      <td>CHEMBL4293155</td>\n",
              "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccccc3Cl)CC...</td>\n",
              "      <td>2440.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7020</th>\n",
              "      <td>CHEMBL4282558</td>\n",
              "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3cccc(Cl)c3)...</td>\n",
              "      <td>2540.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7021</th>\n",
              "      <td>CHEMBL4281727</td>\n",
              "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(Br)cc3)...</td>\n",
              "      <td>3810.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7022</th>\n",
              "      <td>CHEMBL4292349</td>\n",
              "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3cccc([N+](=...</td>\n",
              "      <td>3460.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7023</th>\n",
              "      <td>CHEMBL4278260</td>\n",
              "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(C#N)cc3...</td>\n",
              "      <td>2780.0</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>4695 rows × 3 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "     molecule_chembl_id  ... standard_value\n",
              "0          CHEMBL133897  ...          750.0\n",
              "1          CHEMBL336398  ...          100.0\n",
              "2          CHEMBL131588  ...        50000.0\n",
              "3          CHEMBL130628  ...          300.0\n",
              "4          CHEMBL130478  ...          800.0\n",
              "...                 ...  ...            ...\n",
              "7019      CHEMBL4293155  ...         2440.0\n",
              "7020      CHEMBL4282558  ...         2540.0\n",
              "7021      CHEMBL4281727  ...         3810.0\n",
              "7022      CHEMBL4292349  ...         3460.0\n",
              "7023      CHEMBL4278260  ...         2780.0\n",
              "\n",
              "[4695 rows x 3 columns]"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 12
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "d0ObVWGmkj_L",
        "colab_type": "text"
      },
      "source": [
        "Saves dataframe to CSV file"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "pAzJTVu4kMd_",
        "colab_type": "code",
        "colab": {}
      },
      "source": [
        "df3.to_csv('acetylcholinesterase_02_bioactivity_data_preprocessed.csv', index=False)"
      ],
      "execution_count": 0,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "tO22XVlzhkXR",
        "colab_type": "text"
      },
      "source": [
        "### **Labeling compounds as either being active, inactive or intermediate**\n",
        "The bioactivity data is in the IC50 unit. Compounds having values of less than 1000 nM will be considered to be **active** while those greater than 10,000 nM will be considered to be **inactive**. As for those values in between 1,000 and 10,000 nM will be referred to as **intermediate**. "
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "Ck9Z2M9CkRy_",
        "colab_type": "code",
        "colab": {}
      },
      "source": [
        "df4 = pd.read_csv('acetylcholinesterase_02_bioactivity_data_preprocessed.csv')"
      ],
      "execution_count": 0,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "1E8rz7oMOd-5",
        "colab_type": "code",
        "colab": {}
      },
      "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\")"
      ],
      "execution_count": 0,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "Li64nUiZQ-y2",
        "colab_type": "code",
        "outputId": "18546d01-c66f-4f6e-aca8-14562339ba17",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 419
        }
      },
      "source": [
        "bioactivity_class = pd.Series(bioactivity_threshold, name='class')\n",
        "df5 = pd.concat([df4, bioactivity_class], axis=1)\n",
        "df5"
      ],
      "execution_count": 0,
      "outputs": [
        {
          "output_type": "execute_result",
          "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>CHEMBL133897</td>\n",
              "      <td>CCOc1nn(-c2cccc(OCc3ccccc3)c2)c(=O)o1</td>\n",
              "      <td>750.0</td>\n",
              "      <td>active</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>CHEMBL336398</td>\n",
              "      <td>O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC1CC1</td>\n",
              "      <td>100.0</td>\n",
              "      <td>active</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>CHEMBL131588</td>\n",
              "      <td>CN(C(=O)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F)c1ccccc1</td>\n",
              "      <td>50000.0</td>\n",
              "      <td>inactive</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>CHEMBL130628</td>\n",
              "      <td>O=C(N1CCCCC1)n1nc(-c2ccc(Cl)cc2)nc1SCC(F)(F)F</td>\n",
              "      <td>300.0</td>\n",
              "      <td>active</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>CHEMBL130478</td>\n",
              "      <td>CSc1nc(-c2ccc(OC(F)(F)F)cc2)nn1C(=O)N(C)C</td>\n",
              "      <td>800.0</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>4690</th>\n",
              "      <td>CHEMBL4293155</td>\n",
              "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccccc3Cl)CC...</td>\n",
              "      <td>2440.0</td>\n",
              "      <td>intermediate</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4691</th>\n",
              "      <td>CHEMBL4282558</td>\n",
              "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3cccc(Cl)c3)...</td>\n",
              "      <td>2540.0</td>\n",
              "      <td>intermediate</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4692</th>\n",
              "      <td>CHEMBL4281727</td>\n",
              "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(Br)cc3)...</td>\n",
              "      <td>3810.0</td>\n",
              "      <td>intermediate</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4693</th>\n",
              "      <td>CHEMBL4292349</td>\n",
              "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3cccc([N+](=...</td>\n",
              "      <td>3460.0</td>\n",
              "      <td>intermediate</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4694</th>\n",
              "      <td>CHEMBL4278260</td>\n",
              "      <td>CC(C)(C)c1cc(/C=C/C(=O)NCCC2CCN(Cc3ccc(C#N)cc3...</td>\n",
              "      <td>2780.0</td>\n",
              "      <td>intermediate</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>4695 rows × 4 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "     molecule_chembl_id  ...         class\n",
              "0          CHEMBL133897  ...        active\n",
              "1          CHEMBL336398  ...        active\n",
              "2          CHEMBL131588  ...      inactive\n",
              "3          CHEMBL130628  ...        active\n",
              "4          CHEMBL130478  ...        active\n",
              "...                 ...  ...           ...\n",
              "4690      CHEMBL4293155  ...  intermediate\n",
              "4691      CHEMBL4282558  ...  intermediate\n",
              "4692      CHEMBL4281727  ...  intermediate\n",
              "4693      CHEMBL4292349  ...  intermediate\n",
              "4694      CHEMBL4278260  ...  intermediate\n",
              "\n",
              "[4695 rows x 4 columns]"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 16
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "9tlgyexWh7YJ",
        "colab_type": "text"
      },
      "source": [
        "Saves dataframe to CSV file"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "nSNia7suXstR",
        "colab_type": "code",
        "colab": {}
      },
      "source": [
        "df5.to_csv('acetylcholinesterase_03_bioactivity_data_curated.csv', index=False)"
      ],
      "execution_count": 0,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "0eCQTu9MnzyH",
        "colab_type": "code",
        "outputId": "bb0dd61b-5a21-44cb-cb12-f356784c7b7e",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 68
        }
      },
      "source": [
        "! zip acetylcholinesterase.zip *.csv"
      ],
      "execution_count": 0,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "  adding: acetylcholinesterase_01_bioactivity_data_raw.csv (deflated 90%)\n",
            "  adding: acetylcholinesterase_02_bioactivity_data_preprocessed.csv (deflated 81%)\n",
            "  adding: acetylcholinesterase_03_bioactivity_data_curated.csv (deflated 82%)\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "UuZf5-MEd-H5",
        "colab_type": "code",
        "outputId": "d27dac4e-a925-4645-9e0d-ab43127b4eb2",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 119
        }
      },
      "source": [
        "! ls -l"
      ],
      "execution_count": 0,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "total 4668\n",
            "-rw-r--r-- 1 root root 3562870 Jun  1 15:03 acetylcholinesterase_01_bioactivity_data_raw.csv\n",
            "-rw-r--r-- 1 root root  342989 Jun  1 15:03 acetylcholinesterase_02_bioactivity_data_preprocessed.csv\n",
            "-rw-r--r-- 1 root root  385924 Jun  1 15:03 acetylcholinesterase_03_bioactivity_data_curated.csv\n",
            "-rw-r--r-- 1 root root  475843 Jun  1 15:03 acetylcholinesterase.zip\n",
            "drwxr-xr-x 1 root root    4096 May 27 16:27 sample_data\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "ZywB5K_Dlawb",
        "colab_type": "text"
      },
      "source": [
        "---"
      ]
    }
  ]
}