CDD_ML_Part_1_Bioactivity_Data_Beta_Amyloid.ipynb

{
  "nbformat": 4,
  "nbformat_minor": 0,
  "metadata": {
    "colab": {
      "name": "CDD-ML-Part-1-Bioactivity-Data-Beta_Amyloid.ipynb",
      "provenance": [],
      "collapsed_sections": [],
      "include_colab_link": true
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    }
  },
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "view-in-github",
        "colab_type": "text"
      },
      "source": [
        "<a href=\"https://colab.research.google.com/github/ahrbadr/test/blob/master/CDD_ML_Part_1_Bioactivity_Data_Beta_Amyloid.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "wSFbIMb87cHu"
      },
      "source": [
        "# **Computational Drug Discovery [Part 1] Download Bioactivity Data )**\n",
        "\n",
        "\n",
        "\n",
        "In **Part 1**, we will be performing Data Collection and Pre-Processing from the ChEMBL Database.\n",
        "\n",
        "\n",
        "\n",
        "---"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "iryGAwAIQ4yf"
      },
      "source": [
        "## **Installing libraries**"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "toGT1U_B7F2i"
      },
      "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": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "2002f661-8ec0-42b6-e2b3-3cf796c9212b"
      },
      "source": [
        "! pip install chembl_webresource_client"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "Requirement already satisfied: chembl_webresource_client in /usr/local/lib/python3.7/dist-packages (0.10.4)\n",
            "Requirement already satisfied: urllib3 in /usr/local/lib/python3.7/dist-packages (from chembl_webresource_client) (1.24.3)\n",
            "Requirement already satisfied: requests>=2.18.4 in /usr/local/lib/python3.7/dist-packages (from chembl_webresource_client) (2.23.0)\n",
            "Requirement already satisfied: requests-cache>=0.6.0 in /usr/local/lib/python3.7/dist-packages (from chembl_webresource_client) (0.6.4)\n",
            "Requirement already satisfied: easydict in /usr/local/lib/python3.7/dist-packages (from chembl_webresource_client) (1.9)\n",
            "Requirement already satisfied: idna<3,>=2.5 in /usr/local/lib/python3.7/dist-packages (from requests>=2.18.4->chembl_webresource_client) (2.10)\n",
            "Requirement already satisfied: chardet<4,>=3.0.2 in /usr/local/lib/python3.7/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/python3.7/dist-packages (from requests>=2.18.4->chembl_webresource_client) (2021.5.30)\n",
            "Requirement already satisfied: url-normalize>=1.4 in /usr/local/lib/python3.7/dist-packages (from requests-cache>=0.6.0->chembl_webresource_client) (1.4.3)\n",
            "Requirement already satisfied: itsdangerous in /usr/local/lib/python3.7/dist-packages (from requests-cache>=0.6.0->chembl_webresource_client) (1.1.0)\n",
            "Requirement already satisfied: six in /usr/local/lib/python3.7/dist-packages (from url-normalize>=1.4->requests-cache>=0.6.0->chembl_webresource_client) (1.15.0)\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "J0kJjL8gb5nX"
      },
      "source": [
        "## **Importing libraries**"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "RXoCvMPPfNrv"
      },
      "source": [
        "# Import necessary libraries\n",
        "import pandas as pd\n",
        "from chembl_webresource_client.new_client import new_client"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "1FgUai1bfigC"
      },
      "source": [
        "## **Search for Target protein**"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "7lBsDrD0gAqH"
      },
      "source": [
        "### **Target search for Beta_Amyloid**"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "Vxtp79so4ZjF",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 589
        },
        "outputId": "199ebb08-2ae6-448c-876f-9603d94acb9a"
      },
      "source": [
        "# Target search for Beta_Amyloid\n",
        "target = new_client.target\n",
        "target_query = target.search('beta amyloid')\n",
        "targets = pd.DataFrame.from_dict(target_query)\n",
        "targets"
      ],
      "execution_count": null,
      "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>cross_references</th>\n",
              "      <th>organism</th>\n",
              "      <th>pref_name</th>\n",
              "      <th>score</th>\n",
              "      <th>species_group_flag</th>\n",
              "      <th>target_chembl_id</th>\n",
              "      <th>target_components</th>\n",
              "      <th>target_type</th>\n",
              "      <th>tax_id</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>[{'xref_id': 'P05067', 'xref_name': None, 'xre...</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</td>\n",
              "      <td>19.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>[{'accession': 'P05067', 'component_descriptio...</td>\n",
              "      <td>SINGLE PROTEIN</td>\n",
              "      <td>9606.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>[]</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Amyloid beta-binding alcohol dehydrogenase</td>\n",
              "      <td>19.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL4295598</td>\n",
              "      <td>[{'accession': 'Q2L8D9', 'component_descriptio...</td>\n",
              "      <td>SINGLE PROTEIN</td>\n",
              "      <td>9606.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>[]</td>\n",
              "      <td>Mus musculus</td>\n",
              "      <td>Amyloid-beta A4 protein</td>\n",
              "      <td>19.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL4523942</td>\n",
              "      <td>[{'accession': 'P12023', 'component_descriptio...</td>\n",
              "      <td>SINGLE PROTEIN</td>\n",
              "      <td>10090.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>[{'xref_id': 'P37840', 'xref_name': None, 'xre...</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Alpha-synuclein</td>\n",
              "      <td>18.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL6152</td>\n",
              "      <td>[{'accession': 'P37840', 'component_descriptio...</td>\n",
              "      <td>SINGLE PROTEIN</td>\n",
              "      <td>9606.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>[]</td>\n",
              "      <td>Rattus norvegicus</td>\n",
              "      <td>Amyloid beta A4 protein</td>\n",
              "      <td>18.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL3638365</td>\n",
              "      <td>[{'accession': 'P08592', 'component_descriptio...</td>\n",
              "      <td>SINGLE PROTEIN</td>\n",
              "      <td>10116.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>...</th>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1100</th>\n",
              "      <td>[]</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>3',5'-cyclic phosphodiesterase</td>\n",
              "      <td>1.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL2363066</td>\n",
              "      <td>[{'accession': 'O76074', 'component_descriptio...</td>\n",
              "      <td>PROTEIN FAMILY</td>\n",
              "      <td>9606.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1101</th>\n",
              "      <td>[]</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Caspase</td>\n",
              "      <td>1.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL3831289</td>\n",
              "      <td>[{'accession': 'P49662', 'component_descriptio...</td>\n",
              "      <td>PROTEIN FAMILY</td>\n",
              "      <td>9606.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1102</th>\n",
              "      <td>[]</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>mTORC2</td>\n",
              "      <td>1.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL4523999</td>\n",
              "      <td>[{'accession': 'P42345', 'component_descriptio...</td>\n",
              "      <td>PROTEIN COMPLEX</td>\n",
              "      <td>9606.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1103</th>\n",
              "      <td>[{'xref_id': 'C3TDZ2', 'xref_name': None, 'xre...</td>\n",
              "      <td>Escherichia coli</td>\n",
              "      <td>3-oxoacyl-[acyl-carrier-protein] synthase 3</td>\n",
              "      <td>0.0</td>\n",
              "      <td>False</td>\n",
              "      <td>CHEMBL1795135</td>\n",
              "      <td>[{'accession': 'C3TDZ2', 'component_descriptio...</td>\n",
              "      <td>SINGLE PROTEIN</td>\n",
              "      <td>562.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1104</th>\n",
              "      <td>[]</td>\n",
              "      <td>Bacteria</td>\n",
              "      <td>Bacterial 70S ribosome</td>\n",
              "      <td>0.0</td>\n",
              "      <td>True</td>\n",
              "      <td>CHEMBL2363135</td>\n",
              "      <td>[{'accession': 'P0A7V0', 'component_descriptio...</td>\n",
              "      <td>PROTEIN NUCLEIC-ACID COMPLEX</td>\n",
              "      <td>2.0</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>1105 rows × 9 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "                                       cross_references  ...   tax_id\n",
              "0     [{'xref_id': 'P05067', 'xref_name': None, 'xre...  ...   9606.0\n",
              "1                                                    []  ...   9606.0\n",
              "2                                                    []  ...  10090.0\n",
              "3     [{'xref_id': 'P37840', 'xref_name': None, 'xre...  ...   9606.0\n",
              "4                                                    []  ...  10116.0\n",
              "...                                                 ...  ...      ...\n",
              "1100                                                 []  ...   9606.0\n",
              "1101                                                 []  ...   9606.0\n",
              "1102                                                 []  ...   9606.0\n",
              "1103  [{'xref_id': 'C3TDZ2', 'xref_name': None, 'xre...  ...    562.0\n",
              "1104                                                 []  ...      2.0\n",
              "\n",
              "[1105 rows x 9 columns]"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 25
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "Y5OPfEALjAfZ"
      },
      "source": [
        "### **Select and retrieve bioactivity data for *Human Beta_Amyloid* (first entry)**"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "gSQ3aroOgML7"
      },
      "source": [
        "We will assign the first entry (which corresponds to the target protein, *Human Beta_Amyloid*) to the ***selected_target*** variable "
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "StrcHMVLha7u",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 35
        },
        "outputId": "5de7de3c-1e5a-4843-a13e-49155f6e2347"
      },
      "source": [
        "selected_target = targets.target_chembl_id[0]\n",
        "selected_target"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "application/vnd.google.colaboratory.intrinsic+json": {
              "type": "string"
            },
            "text/plain": [
              "'CHEMBL2487'"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 26
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "GWd2DRalgjzB"
      },
      "source": [
        "Here, we will retrieve only bioactivity data for *Human Beta_Amyloid* (CHEMBL2487) that are reported as pChEMBL values."
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "LeFbV_CsSP8D"
      },
      "source": [
        "activity = new_client.activity\n",
        "res = activity.filter(target_chembl_id=selected_target).filter(standard_type=\"IC50\")"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "LrzAcEFnYzBY"
      },
      "source": [
        "df = pd.DataFrame.from_dict(res)"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "s9iUAXFdSkoM",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 694
        },
        "outputId": "adfb5dc5-100a-4b66-d920-174c4b03f94a"
      },
      "source": [
        "df"
      ],
      "execution_count": null,
      "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>assay_variant_accession</th>\n",
              "      <th>assay_variant_mutation</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>357577</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL678443</td>\n",
              "      <td>Inhibition of A-beta-42 production by inhibiti...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000219</td>\n",
              "      <td>cell-based format</td>\n",
              "      <td>CC12CCC(C1)C(C)(C)C2NS(=O)(=O)c1ccc(F)cc1</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1133739</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2000.0</td>\n",
              "      <td>{'bei': '17.02', 'le': '0.34', 'lle': '1.98', ...</td>\n",
              "      <td>CHEMBL311039</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL311039</td>\n",
              "      <td>5.30</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>132837</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>5000.0</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</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>5.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>None</td>\n",
              "      <td>357580</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL678443</td>\n",
              "      <td>Inhibition of A-beta-42 production by inhibiti...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000219</td>\n",
              "      <td>cell-based format</td>\n",
              "      <td>CC12CC[C@@H](C1)C(C)(C)[C@@H]2NS(=O)(=O)c1cccs1</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1133739</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2000.0</td>\n",
              "      <td>{'bei': '18.60', 'le': '0.40', 'lle': '2.33', ...</td>\n",
              "      <td>CHEMBL450926</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL450926</td>\n",
              "      <td>5.57</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>132839</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>2700.0</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</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>2.7</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>None</td>\n",
              "      <td>358965</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL678443</td>\n",
              "      <td>Inhibition of A-beta-42 production by inhibiti...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000219</td>\n",
              "      <td>cell-based format</td>\n",
              "      <td>CC12CC[C@@H](C1)C(C)(C)[C@@H]2NS(=O)(=O)c1ccc(...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1133739</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2000.0</td>\n",
              "      <td>{'bei': '18.45', 'le': '0.37', 'lle': '2.42', ...</td>\n",
              "      <td>CHEMBL310242</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL310242</td>\n",
              "      <td>5.75</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>132841</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>1800.0</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</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>1.8</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>None</td>\n",
              "      <td>368887</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL678443</td>\n",
              "      <td>Inhibition of A-beta-42 production by inhibiti...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000219</td>\n",
              "      <td>cell-based format</td>\n",
              "      <td>CC12CC[C@@H](C1)C(C)(C)[C@@H]2NS(=O)(=O)c1ccc(...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1133739</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2000.0</td>\n",
              "      <td>{'bei': '15.12', 'le': '0.32', 'lle': '1.13', ...</td>\n",
              "      <td>CHEMBL74874</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL74874</td>\n",
              "      <td>4.96</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>132840</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>11000.0</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</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>11.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>None</td>\n",
              "      <td>375954</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL678443</td>\n",
              "      <td>Inhibition of A-beta-42 production by inhibiti...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000219</td>\n",
              "      <td>cell-based format</td>\n",
              "      <td>CC12CC[C@@H](C1)C(C)(C)[C@@H]2NS(=O)(=O)c1ccc(...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1133739</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2000.0</td>\n",
              "      <td>{'bei': '13.43', 'le': '0.33', 'lle': '1.06', ...</td>\n",
              "      <td>CHEMBL75183</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL75183</td>\n",
              "      <td>5.00</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>132838</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>10000.0</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</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>10.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>...</th>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <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>1229</th>\n",
              "      <td>Not Active</td>\n",
              "      <td>20120045</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4510291</td>\n",
              "      <td>APP40 inhibition assay</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>CC(C)(C)OC(=O)N1CCCC1CNC1CCC(c2cc(F)ccc2F)(S(=...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4507288</td>\n",
              "      <td>None</td>\n",
              "      <td>NaN</td>\n",
              "      <td>{'bei': '10.18', 'le': '0.21', 'lle': '-0.42',...</td>\n",
              "      <td>CHEMBL4558518</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4558518</td>\n",
              "      <td>5.80</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3359706</td>\n",
              "      <td>=</td>\n",
              "      <td>54</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>1600.0</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</td>\n",
              "      <td>9606</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>UO_0000065</td>\n",
              "      <td>None</td>\n",
              "      <td>1600.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1230</th>\n",
              "      <td>Active</td>\n",
              "      <td>20120642</td>\n",
              "      <td>[{'comments': None, 'relation': None, 'result_...</td>\n",
              "      <td>CHEMBL4510293</td>\n",
              "      <td>APP42 inhibition assay</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>COc1cc(-c2cn(C3CCc4c(F)cccc4N(CC(F)(F)F)C3=O)n...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4507289</td>\n",
              "      <td>None</td>\n",
              "      <td>NaN</td>\n",
              "      <td>{'bei': '14.59', 'le': '0.28', 'lle': '2.84', ...</td>\n",
              "      <td>CHEMBL3609637</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL3609637</td>\n",
              "      <td>7.51</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3359707</td>\n",
              "      <td>=</td>\n",
              "      <td>54</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>31.0</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</td>\n",
              "      <td>9606</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>UO_0000065</td>\n",
              "      <td>None</td>\n",
              "      <td>31.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1231</th>\n",
              "      <td>Active</td>\n",
              "      <td>20120643</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4510294</td>\n",
              "      <td>APP40 inhibition assay</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>COc1cc(-c2cn(C3CCc4c(F)cccc4N(CC(F)(F)F)C3=O)n...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4507289</td>\n",
              "      <td>None</td>\n",
              "      <td>NaN</td>\n",
              "      <td>{'bei': '13.38', 'le': '0.25', 'lle': '2.21', ...</td>\n",
              "      <td>CHEMBL3609637</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL3609637</td>\n",
              "      <td>6.88</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3359707</td>\n",
              "      <td>=</td>\n",
              "      <td>54</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>131.0</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</td>\n",
              "      <td>9606</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>UO_0000065</td>\n",
              "      <td>None</td>\n",
              "      <td>131.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1232</th>\n",
              "      <td>Not Active</td>\n",
              "      <td>20120647</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4510293</td>\n",
              "      <td>APP42 inhibition assay</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>COc1cc(-c2cn(C3CCc4ccccc4N(CC(F)(F)F)C3=O)nn2)...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4507289</td>\n",
              "      <td>None</td>\n",
              "      <td>NaN</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4534005</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4534005</td>\n",
              "      <td>None</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3359708</td>\n",
              "      <td>&gt;</td>\n",
              "      <td>54</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>10000.0</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</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>10.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1233</th>\n",
              "      <td>Not Active</td>\n",
              "      <td>20120648</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4510294</td>\n",
              "      <td>APP40 inhibition assay</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>COc1cc(-c2cn(C3CCc4ccccc4N(CC(F)(F)F)C3=O)nn2)...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4507289</td>\n",
              "      <td>None</td>\n",
              "      <td>NaN</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4534005</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4534005</td>\n",
              "      <td>None</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3359708</td>\n",
              "      <td>&gt;</td>\n",
              "      <td>54</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>10000.0</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</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>10.0</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>1234 rows × 45 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "     activity_comment  activity_id  ... upper_value   value\n",
              "0                None       357577  ...        None     5.0\n",
              "1                None       357580  ...        None     2.7\n",
              "2                None       358965  ...        None     1.8\n",
              "3                None       368887  ...        None    11.0\n",
              "4                None       375954  ...        None    10.0\n",
              "...               ...          ...  ...         ...     ...\n",
              "1229       Not Active     20120045  ...        None  1600.0\n",
              "1230           Active     20120642  ...        None    31.0\n",
              "1231           Active     20120643  ...        None   131.0\n",
              "1232       Not Active     20120647  ...        None    10.0\n",
              "1233       Not Active     20120648  ...        None    10.0\n",
              "\n",
              "[1234 rows x 45 columns]"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 29
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "fQ78N26Fg15T"
      },
      "source": [
        "Finally we will save the resulting bioactivity data to a CSV file **bioactivity_data.csv**."
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "ZvUUEIVxTOH1"
      },
      "source": [
        "df.to_csv('BetaAmyloid_01_bioactivity_data_raw.csv', index=False)"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "_GXMpFNUOn_8"
      },
      "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": {
          "base_uri": "https://localhost:8080/",
          "height": 728
        },
        "outputId": "c2367611-b3d9-4da0-a03c-263255729d30"
      },
      "source": [
        "df2 = df[df.standard_value.notna()]\n",
        "df2 = df2[df.canonical_smiles.notna()]\n",
        "df2"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "/usr/local/lib/python3.7/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>assay_variant_accession</th>\n",
              "      <th>assay_variant_mutation</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>357577</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL678443</td>\n",
              "      <td>Inhibition of A-beta-42 production by inhibiti...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000219</td>\n",
              "      <td>cell-based format</td>\n",
              "      <td>CC12CCC(C1)C(C)(C)C2NS(=O)(=O)c1ccc(F)cc1</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1133739</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2000.0</td>\n",
              "      <td>{'bei': '17.02', 'le': '0.34', 'lle': '1.98', ...</td>\n",
              "      <td>CHEMBL311039</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL311039</td>\n",
              "      <td>5.30</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>132837</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>5000.0</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</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>5.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>None</td>\n",
              "      <td>357580</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL678443</td>\n",
              "      <td>Inhibition of A-beta-42 production by inhibiti...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000219</td>\n",
              "      <td>cell-based format</td>\n",
              "      <td>CC12CC[C@@H](C1)C(C)(C)[C@@H]2NS(=O)(=O)c1cccs1</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1133739</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2000.0</td>\n",
              "      <td>{'bei': '18.60', 'le': '0.40', 'lle': '2.33', ...</td>\n",
              "      <td>CHEMBL450926</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL450926</td>\n",
              "      <td>5.57</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>132839</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>2700.0</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</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>2.7</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>None</td>\n",
              "      <td>358965</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL678443</td>\n",
              "      <td>Inhibition of A-beta-42 production by inhibiti...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000219</td>\n",
              "      <td>cell-based format</td>\n",
              "      <td>CC12CC[C@@H](C1)C(C)(C)[C@@H]2NS(=O)(=O)c1ccc(...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1133739</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2000.0</td>\n",
              "      <td>{'bei': '18.45', 'le': '0.37', 'lle': '2.42', ...</td>\n",
              "      <td>CHEMBL310242</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL310242</td>\n",
              "      <td>5.75</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>132841</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>1800.0</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</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>1.8</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>None</td>\n",
              "      <td>368887</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL678443</td>\n",
              "      <td>Inhibition of A-beta-42 production by inhibiti...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000219</td>\n",
              "      <td>cell-based format</td>\n",
              "      <td>CC12CC[C@@H](C1)C(C)(C)[C@@H]2NS(=O)(=O)c1ccc(...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1133739</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2000.0</td>\n",
              "      <td>{'bei': '15.12', 'le': '0.32', 'lle': '1.13', ...</td>\n",
              "      <td>CHEMBL74874</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL74874</td>\n",
              "      <td>4.96</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>132840</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>11000.0</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</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>11.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>None</td>\n",
              "      <td>375954</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL678443</td>\n",
              "      <td>Inhibition of A-beta-42 production by inhibiti...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000219</td>\n",
              "      <td>cell-based format</td>\n",
              "      <td>CC12CC[C@@H](C1)C(C)(C)[C@@H]2NS(=O)(=O)c1ccc(...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1133739</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2000.0</td>\n",
              "      <td>{'bei': '13.43', 'le': '0.33', 'lle': '1.06', ...</td>\n",
              "      <td>CHEMBL75183</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL75183</td>\n",
              "      <td>5.00</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>132838</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>10000.0</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</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>10.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>...</th>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <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>1229</th>\n",
              "      <td>Not Active</td>\n",
              "      <td>20120045</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4510291</td>\n",
              "      <td>APP40 inhibition assay</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>CC(C)(C)OC(=O)N1CCCC1CNC1CCC(c2cc(F)ccc2F)(S(=...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4507288</td>\n",
              "      <td>None</td>\n",
              "      <td>NaN</td>\n",
              "      <td>{'bei': '10.18', 'le': '0.21', 'lle': '-0.42',...</td>\n",
              "      <td>CHEMBL4558518</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4558518</td>\n",
              "      <td>5.80</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3359706</td>\n",
              "      <td>=</td>\n",
              "      <td>54</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>1600.0</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</td>\n",
              "      <td>9606</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>UO_0000065</td>\n",
              "      <td>None</td>\n",
              "      <td>1600.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1230</th>\n",
              "      <td>Active</td>\n",
              "      <td>20120642</td>\n",
              "      <td>[{'comments': None, 'relation': None, 'result_...</td>\n",
              "      <td>CHEMBL4510293</td>\n",
              "      <td>APP42 inhibition assay</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>COc1cc(-c2cn(C3CCc4c(F)cccc4N(CC(F)(F)F)C3=O)n...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4507289</td>\n",
              "      <td>None</td>\n",
              "      <td>NaN</td>\n",
              "      <td>{'bei': '14.59', 'le': '0.28', 'lle': '2.84', ...</td>\n",
              "      <td>CHEMBL3609637</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL3609637</td>\n",
              "      <td>7.51</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3359707</td>\n",
              "      <td>=</td>\n",
              "      <td>54</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>31.0</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</td>\n",
              "      <td>9606</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>UO_0000065</td>\n",
              "      <td>None</td>\n",
              "      <td>31.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1231</th>\n",
              "      <td>Active</td>\n",
              "      <td>20120643</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4510294</td>\n",
              "      <td>APP40 inhibition assay</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>COc1cc(-c2cn(C3CCc4c(F)cccc4N(CC(F)(F)F)C3=O)n...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4507289</td>\n",
              "      <td>None</td>\n",
              "      <td>NaN</td>\n",
              "      <td>{'bei': '13.38', 'le': '0.25', 'lle': '2.21', ...</td>\n",
              "      <td>CHEMBL3609637</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL3609637</td>\n",
              "      <td>6.88</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3359707</td>\n",
              "      <td>=</td>\n",
              "      <td>54</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>131.0</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</td>\n",
              "      <td>9606</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>UO_0000065</td>\n",
              "      <td>None</td>\n",
              "      <td>131.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1232</th>\n",
              "      <td>Not Active</td>\n",
              "      <td>20120647</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4510293</td>\n",
              "      <td>APP42 inhibition assay</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>COc1cc(-c2cn(C3CCc4ccccc4N(CC(F)(F)F)C3=O)nn2)...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4507289</td>\n",
              "      <td>None</td>\n",
              "      <td>NaN</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4534005</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4534005</td>\n",
              "      <td>None</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3359708</td>\n",
              "      <td>&gt;</td>\n",
              "      <td>54</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>10000.0</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</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>10.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1233</th>\n",
              "      <td>Not Active</td>\n",
              "      <td>20120648</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4510294</td>\n",
              "      <td>APP40 inhibition assay</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>COc1cc(-c2cn(C3CCc4ccccc4N(CC(F)(F)F)C3=O)nn2)...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4507289</td>\n",
              "      <td>None</td>\n",
              "      <td>NaN</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4534005</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4534005</td>\n",
              "      <td>None</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3359708</td>\n",
              "      <td>&gt;</td>\n",
              "      <td>54</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>10000.0</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</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>10.0</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>1106 rows × 45 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "     activity_comment  activity_id  ... upper_value   value\n",
              "0                None       357577  ...        None     5.0\n",
              "1                None       357580  ...        None     2.7\n",
              "2                None       358965  ...        None     1.8\n",
              "3                None       368887  ...        None    11.0\n",
              "4                None       375954  ...        None    10.0\n",
              "...               ...          ...  ...         ...     ...\n",
              "1229       Not Active     20120045  ...        None  1600.0\n",
              "1230           Active     20120642  ...        None    31.0\n",
              "1231           Active     20120643  ...        None   131.0\n",
              "1232       Not Active     20120647  ...        None    10.0\n",
              "1233       Not Active     20120648  ...        None    10.0\n",
              "\n",
              "[1106 rows x 45 columns]"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 32
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "wCkuaeVNbdtM",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "83b04bfb-0fad-4387-d7e8-fb435ef27f64"
      },
      "source": [
        "len(df2.canonical_smiles.unique())"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "929"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 33
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "JbAK3K7wclkS",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 694
        },
        "outputId": "15d6cd69-f49c-4104-bc38-32e34a09c610"
      },
      "source": [
        "df2_nr = df2.drop_duplicates(['canonical_smiles'])\n",
        "df2_nr"
      ],
      "execution_count": null,
      "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>assay_variant_accession</th>\n",
              "      <th>assay_variant_mutation</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>357577</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL678443</td>\n",
              "      <td>Inhibition of A-beta-42 production by inhibiti...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000219</td>\n",
              "      <td>cell-based format</td>\n",
              "      <td>CC12CCC(C1)C(C)(C)C2NS(=O)(=O)c1ccc(F)cc1</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1133739</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2000.0</td>\n",
              "      <td>{'bei': '17.02', 'le': '0.34', 'lle': '1.98', ...</td>\n",
              "      <td>CHEMBL311039</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL311039</td>\n",
              "      <td>5.30</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>132837</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>5000.0</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</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>5.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>None</td>\n",
              "      <td>357580</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL678443</td>\n",
              "      <td>Inhibition of A-beta-42 production by inhibiti...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000219</td>\n",
              "      <td>cell-based format</td>\n",
              "      <td>CC12CC[C@@H](C1)C(C)(C)[C@@H]2NS(=O)(=O)c1cccs1</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1133739</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2000.0</td>\n",
              "      <td>{'bei': '18.60', 'le': '0.40', 'lle': '2.33', ...</td>\n",
              "      <td>CHEMBL450926</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL450926</td>\n",
              "      <td>5.57</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>132839</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>2700.0</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</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>2.7</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>None</td>\n",
              "      <td>358965</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL678443</td>\n",
              "      <td>Inhibition of A-beta-42 production by inhibiti...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000219</td>\n",
              "      <td>cell-based format</td>\n",
              "      <td>CC12CC[C@@H](C1)C(C)(C)[C@@H]2NS(=O)(=O)c1ccc(...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1133739</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2000.0</td>\n",
              "      <td>{'bei': '18.45', 'le': '0.37', 'lle': '2.42', ...</td>\n",
              "      <td>CHEMBL310242</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL310242</td>\n",
              "      <td>5.75</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>132841</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>1800.0</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</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>1.8</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>None</td>\n",
              "      <td>368887</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL678443</td>\n",
              "      <td>Inhibition of A-beta-42 production by inhibiti...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000219</td>\n",
              "      <td>cell-based format</td>\n",
              "      <td>CC12CC[C@@H](C1)C(C)(C)[C@@H]2NS(=O)(=O)c1ccc(...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1133739</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2000.0</td>\n",
              "      <td>{'bei': '15.12', 'le': '0.32', 'lle': '1.13', ...</td>\n",
              "      <td>CHEMBL74874</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL74874</td>\n",
              "      <td>4.96</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>132840</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>11000.0</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</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>11.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>None</td>\n",
              "      <td>375954</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL678443</td>\n",
              "      <td>Inhibition of A-beta-42 production by inhibiti...</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000219</td>\n",
              "      <td>cell-based format</td>\n",
              "      <td>CC12CC[C@@H](C1)C(C)(C)[C@@H]2NS(=O)(=O)c1ccc(...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1133739</td>\n",
              "      <td>J. Med. Chem.</td>\n",
              "      <td>2000.0</td>\n",
              "      <td>{'bei': '13.43', 'le': '0.33', 'lle': '1.06', ...</td>\n",
              "      <td>CHEMBL75183</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL75183</td>\n",
              "      <td>5.00</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>132838</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>10000.0</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</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>10.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>...</th>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <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>1224</th>\n",
              "      <td>None</td>\n",
              "      <td>19258715</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4403499</td>\n",
              "      <td>Inhibition of beta amyloid in human SH-SY5Y cells</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000219</td>\n",
              "      <td>cell-based format</td>\n",
              "      <td>O=c1oc2c(O)c(O)cc3c(=O)oc4c(O)c(O)cc1c4c23</td>\n",
              "      <td>Outside typical range</td>\n",
              "      <td>Values for this activity type are unusually la...</td>\n",
              "      <td>CHEMBL4402535</td>\n",
              "      <td>Eur J Med Chem</td>\n",
              "      <td>2019.0</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL6246</td>\n",
              "      <td>ELLAGIC ACID</td>\n",
              "      <td>CHEMBL6246</td>\n",
              "      <td>None</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3215485</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>300000.0</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</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>300.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1226</th>\n",
              "      <td>Active</td>\n",
              "      <td>20120042</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4510290</td>\n",
              "      <td>APP42 inhibition assay</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>O=S(=O)(NC1CCC(c2cc(F)ccc2F)(S(=O)(=O)c2ccc(Cl...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4507288</td>\n",
              "      <td>None</td>\n",
              "      <td>NaN</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1091513</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL1091513</td>\n",
              "      <td>None</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3359705</td>\n",
              "      <td>&lt;</td>\n",
              "      <td>54</td>\n",
              "      <td>True</td>\n",
              "      <td>&lt;</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>None</td>\n",
              "      <td>0.5</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</td>\n",
              "      <td>9606</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>UO_0000065</td>\n",
              "      <td>None</td>\n",
              "      <td>0.5</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1229</th>\n",
              "      <td>Not Active</td>\n",
              "      <td>20120045</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4510291</td>\n",
              "      <td>APP40 inhibition assay</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>CC(C)(C)OC(=O)N1CCCC1CNC1CCC(c2cc(F)ccc2F)(S(=...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4507288</td>\n",
              "      <td>None</td>\n",
              "      <td>NaN</td>\n",
              "      <td>{'bei': '10.18', 'le': '0.21', 'lle': '-0.42',...</td>\n",
              "      <td>CHEMBL4558518</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4558518</td>\n",
              "      <td>5.80</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3359706</td>\n",
              "      <td>=</td>\n",
              "      <td>54</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>1600.0</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</td>\n",
              "      <td>9606</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>UO_0000065</td>\n",
              "      <td>None</td>\n",
              "      <td>1600.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1230</th>\n",
              "      <td>Active</td>\n",
              "      <td>20120642</td>\n",
              "      <td>[{'comments': None, 'relation': None, 'result_...</td>\n",
              "      <td>CHEMBL4510293</td>\n",
              "      <td>APP42 inhibition assay</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>COc1cc(-c2cn(C3CCc4c(F)cccc4N(CC(F)(F)F)C3=O)n...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4507289</td>\n",
              "      <td>None</td>\n",
              "      <td>NaN</td>\n",
              "      <td>{'bei': '14.59', 'le': '0.28', 'lle': '2.84', ...</td>\n",
              "      <td>CHEMBL3609637</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL3609637</td>\n",
              "      <td>7.51</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3359707</td>\n",
              "      <td>=</td>\n",
              "      <td>54</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>31.0</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</td>\n",
              "      <td>9606</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>IC50</td>\n",
              "      <td>nM</td>\n",
              "      <td>UO_0000065</td>\n",
              "      <td>None</td>\n",
              "      <td>31.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1232</th>\n",
              "      <td>Not Active</td>\n",
              "      <td>20120647</td>\n",
              "      <td>[]</td>\n",
              "      <td>CHEMBL4510293</td>\n",
              "      <td>APP42 inhibition assay</td>\n",
              "      <td>B</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>BAO_0000190</td>\n",
              "      <td>BAO_0000357</td>\n",
              "      <td>single protein format</td>\n",
              "      <td>COc1cc(-c2cn(C3CCc4ccccc4N(CC(F)(F)F)C3=O)nn2)...</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4507289</td>\n",
              "      <td>None</td>\n",
              "      <td>NaN</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4534005</td>\n",
              "      <td>None</td>\n",
              "      <td>CHEMBL4534005</td>\n",
              "      <td>None</td>\n",
              "      <td>False</td>\n",
              "      <td>http://www.openphacts.org/units/Nanomolar</td>\n",
              "      <td>3359708</td>\n",
              "      <td>&gt;</td>\n",
              "      <td>54</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>10000.0</td>\n",
              "      <td>CHEMBL2487</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>Beta amyloid A4 protein</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>10.0</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>929 rows × 45 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "     activity_comment  activity_id  ... upper_value   value\n",
              "0                None       357577  ...        None     5.0\n",
              "1                None       357580  ...        None     2.7\n",
              "2                None       358965  ...        None     1.8\n",
              "3                None       368887  ...        None    11.0\n",
              "4                None       375954  ...        None    10.0\n",
              "...               ...          ...  ...         ...     ...\n",
              "1224             None     19258715  ...        None   300.0\n",
              "1226           Active     20120042  ...        None     0.5\n",
              "1229       Not Active     20120045  ...        None  1600.0\n",
              "1230           Active     20120642  ...        None    31.0\n",
              "1232       Not Active     20120647  ...        None    10.0\n",
              "\n",
              "[929 rows x 45 columns]"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 35
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "5H4sSFAWhV9B"
      },
      "source": [
        "## **Data pre-processing of the bioactivity data**"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "Nv2dzid_hzKd"
      },
      "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": {
          "base_uri": "https://localhost:8080/",
          "height": 419
        },
        "outputId": "1d5df3c5-b850-404c-9546-606c5138c489"
      },
      "source": [
        "selection = ['molecule_chembl_id','canonical_smiles','standard_value']\n",
        "df3 = df2_nr[selection]\n",
        "df3"
      ],
      "execution_count": null,
      "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",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>CHEMBL311039</td>\n",
              "      <td>CC12CCC(C1)C(C)(C)C2NS(=O)(=O)c1ccc(F)cc1</td>\n",
              "      <td>5000.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>CHEMBL450926</td>\n",
              "      <td>CC12CC[C@@H](C1)C(C)(C)[C@@H]2NS(=O)(=O)c1cccs1</td>\n",
              "      <td>2700.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>CHEMBL310242</td>\n",
              "      <td>CC12CC[C@@H](C1)C(C)(C)[C@@H]2NS(=O)(=O)c1ccc(...</td>\n",
              "      <td>1800.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>CHEMBL74874</td>\n",
              "      <td>CC12CC[C@@H](C1)C(C)(C)[C@@H]2NS(=O)(=O)c1ccc(...</td>\n",
              "      <td>11000.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>CHEMBL75183</td>\n",
              "      <td>CC12CC[C@@H](C1)C(C)(C)[C@@H]2NS(=O)(=O)c1ccc(...</td>\n",
              "      <td>10000.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>...</th>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1224</th>\n",
              "      <td>CHEMBL6246</td>\n",
              "      <td>O=c1oc2c(O)c(O)cc3c(=O)oc4c(O)c(O)cc1c4c23</td>\n",
              "      <td>300000.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1226</th>\n",
              "      <td>CHEMBL1091513</td>\n",
              "      <td>O=S(=O)(NC1CCC(c2cc(F)ccc2F)(S(=O)(=O)c2ccc(Cl...</td>\n",
              "      <td>0.5</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1229</th>\n",
              "      <td>CHEMBL4558518</td>\n",
              "      <td>CC(C)(C)OC(=O)N1CCCC1CNC1CCC(c2cc(F)ccc2F)(S(=...</td>\n",
              "      <td>1600.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1230</th>\n",
              "      <td>CHEMBL3609637</td>\n",
              "      <td>COc1cc(-c2cn(C3CCc4c(F)cccc4N(CC(F)(F)F)C3=O)n...</td>\n",
              "      <td>31.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1232</th>\n",
              "      <td>CHEMBL4534005</td>\n",
              "      <td>COc1cc(-c2cn(C3CCc4ccccc4N(CC(F)(F)F)C3=O)nn2)...</td>\n",
              "      <td>10000.0</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>929 rows × 3 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "     molecule_chembl_id  ... standard_value\n",
              "0          CHEMBL311039  ...         5000.0\n",
              "1          CHEMBL450926  ...         2700.0\n",
              "2          CHEMBL310242  ...         1800.0\n",
              "3           CHEMBL74874  ...        11000.0\n",
              "4           CHEMBL75183  ...        10000.0\n",
              "...                 ...  ...            ...\n",
              "1224         CHEMBL6246  ...       300000.0\n",
              "1226      CHEMBL1091513  ...            0.5\n",
              "1229      CHEMBL4558518  ...         1600.0\n",
              "1230      CHEMBL3609637  ...           31.0\n",
              "1232      CHEMBL4534005  ...        10000.0\n",
              "\n",
              "[929 rows x 3 columns]"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 36
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "d0ObVWGmkj_L"
      },
      "source": [
        "Saves dataframe to CSV file"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "pAzJTVu4kMd_"
      },
      "source": [
        "df3.to_csv('BetaAmyloid_02_bioactivity_data_preprocessed.csv', index=False)"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "tO22XVlzhkXR"
      },
      "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_"
      },
      "source": [
        "df4 = pd.read_csv('BetaAmyloid_02_bioactivity_data_preprocessed.csv')"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "1E8rz7oMOd-5"
      },
      "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": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "Li64nUiZQ-y2",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 419
        },
        "outputId": "e624efa5-c0e5-4f05-d429-f4511502bda7"
      },
      "source": [
        "bioactivity_class = pd.Series(bioactivity_threshold, name='class')\n",
        "df5 = pd.concat([df4, bioactivity_class], axis=1)\n",
        "df5"
      ],
      "execution_count": null,
      "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>CHEMBL311039</td>\n",
              "      <td>CC12CCC(C1)C(C)(C)C2NS(=O)(=O)c1ccc(F)cc1</td>\n",
              "      <td>5000.0</td>\n",
              "      <td>intermediate</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>CHEMBL450926</td>\n",
              "      <td>CC12CC[C@@H](C1)C(C)(C)[C@@H]2NS(=O)(=O)c1cccs1</td>\n",
              "      <td>2700.0</td>\n",
              "      <td>intermediate</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>CHEMBL310242</td>\n",
              "      <td>CC12CC[C@@H](C1)C(C)(C)[C@@H]2NS(=O)(=O)c1ccc(...</td>\n",
              "      <td>1800.0</td>\n",
              "      <td>intermediate</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>CHEMBL74874</td>\n",
              "      <td>CC12CC[C@@H](C1)C(C)(C)[C@@H]2NS(=O)(=O)c1ccc(...</td>\n",
              "      <td>11000.0</td>\n",
              "      <td>inactive</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>CHEMBL75183</td>\n",
              "      <td>CC12CC[C@@H](C1)C(C)(C)[C@@H]2NS(=O)(=O)c1ccc(...</td>\n",
              "      <td>10000.0</td>\n",
              "      <td>inactive</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>924</th>\n",
              "      <td>CHEMBL6246</td>\n",
              "      <td>O=c1oc2c(O)c(O)cc3c(=O)oc4c(O)c(O)cc1c4c23</td>\n",
              "      <td>300000.0</td>\n",
              "      <td>inactive</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>925</th>\n",
              "      <td>CHEMBL1091513</td>\n",
              "      <td>O=S(=O)(NC1CCC(c2cc(F)ccc2F)(S(=O)(=O)c2ccc(Cl...</td>\n",
              "      <td>0.5</td>\n",
              "      <td>active</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>926</th>\n",
              "      <td>CHEMBL4558518</td>\n",
              "      <td>CC(C)(C)OC(=O)N1CCCC1CNC1CCC(c2cc(F)ccc2F)(S(=...</td>\n",
              "      <td>1600.0</td>\n",
              "      <td>intermediate</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>927</th>\n",
              "      <td>CHEMBL3609637</td>\n",
              "      <td>COc1cc(-c2cn(C3CCc4c(F)cccc4N(CC(F)(F)F)C3=O)n...</td>\n",
              "      <td>31.0</td>\n",
              "      <td>active</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>928</th>\n",
              "      <td>CHEMBL4534005</td>\n",
              "      <td>COc1cc(-c2cn(C3CCc4ccccc4N(CC(F)(F)F)C3=O)nn2)...</td>\n",
              "      <td>10000.0</td>\n",
              "      <td>inactive</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>929 rows × 4 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "    molecule_chembl_id  ...         class\n",
              "0         CHEMBL311039  ...  intermediate\n",
              "1         CHEMBL450926  ...  intermediate\n",
              "2         CHEMBL310242  ...  intermediate\n",
              "3          CHEMBL74874  ...      inactive\n",
              "4          CHEMBL75183  ...      inactive\n",
              "..                 ...  ...           ...\n",
              "924         CHEMBL6246  ...      inactive\n",
              "925      CHEMBL1091513  ...        active\n",
              "926      CHEMBL4558518  ...  intermediate\n",
              "927      CHEMBL3609637  ...        active\n",
              "928      CHEMBL4534005  ...      inactive\n",
              "\n",
              "[929 rows x 4 columns]"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 40
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "9tlgyexWh7YJ"
      },
      "source": [
        "Saves dataframe to CSV file"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "nSNia7suXstR"
      },
      "source": [
        "df5.to_csv('BetaAmyloid_03_bioactivity_data_curated.csv', index=False)"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "0eCQTu9MnzyH",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "426bc178-b9b1-4961-b5eb-87ec4ac82a82"
      },
      "source": [
        "! zip BetaAmyloid.zip *.csv"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "  adding: acetylcholinesterase_01_bioactivity_data_raw.csv (deflated 92%)\n",
            "  adding: acetylcholinesterase_02_bioactivity_data_preprocessed.csv (deflated 81%)\n",
            "  adding: acetylcholinesterase_03_bioactivity_data_curated.csv (deflated 82%)\n",
            "  adding: BetaAmyloid_01_bioactivity_data_raw.csv (deflated 92%)\n",
            "  adding: BetaAmyloid_02_bioactivity_data_preprocessed.csv (deflated 81%)\n",
            "  adding: BetaAmyloid_03_bioactivity_data_curated.csv (deflated 82%)\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "UuZf5-MEd-H5",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "eaa693c6-f68c-46d6-a6a7-dc0b8a29bb73"
      },
      "source": [
        "! ls -l"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "total 2148\n",
            "-rw-r--r-- 1 root root 754885 Jun 20 21:37 acetylcholinesterase_01_bioactivity_data_raw.csv\n",
            "-rw-r--r-- 1 root root  72657 Jun 20 21:37 acetylcholinesterase_02_bioactivity_data_preprocessed.csv\n",
            "-rw-r--r-- 1 root root  81186 Jun 20 21:37 acetylcholinesterase_03_bioactivity_data_curated.csv\n",
            "-rw-r--r-- 1 root root 181904 Jun 21 00:08 acetylcholinesterase.zip\n",
            "-rw-r--r-- 1 root root 754885 Jun 20 23:58 BetaAmyloid_01_bioactivity_data_raw.csv\n",
            "-rw-r--r-- 1 root root  72657 Jun 21 00:03 BetaAmyloid_02_bioactivity_data_preprocessed.csv\n",
            "-rw-r--r-- 1 root root  81186 Jun 21 00:08 BetaAmyloid_03_bioactivity_data_curated.csv\n",
            "-rw-r--r-- 1 root root 181904 Jun 21 00:09 BetaAmyloid.zip\n",
            "drwxr-xr-x 1 root root   4096 Jun 15 13:37 sample_data\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "ZywB5K_Dlawb"
      },
      "source": [
        "---"
      ]
    }
  ]
}