{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import pathlib\n",
    "path = pathlib.Path(\"/home/ubuntu/giovanni\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "sim_df = pd.read_csv(path/\"code/2024_Chandrasekaran_NatureMethods/benchmark/output/compound_genetic_perturbation_cosine_similarity.csv\")\n",
    "jump_metadata = pd.read_csv(path/\"code/2024_Chandrasekaran_NatureMethods/metadata/external_metadata/JUMP-Target-1_compound_metadata.tsv\", sep=\"\\t\")\n",
    "\n",
    "sim_df = sim_df.rename(columns={'Metadata_broad_sample': 'broad_sample'})\n",
    "\n",
    "sim_df = pd.merge(\n",
    "    sim_df,\n",
    "    jump_metadata[['broad_sample', 'InChIKey', 'smiles']],\n",
    "    on='broad_sample',\n",
    "    how='left'\n",
    ")\n",
    "\n",
    "sim_df.to_csv(path/\"data/compound_genetic_perturbation_cosine_similarity_inchikey.csv\", index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Metadata_Source</th>\n",
       "      <th>Metadata_Plate</th>\n",
       "      <th>Metadata_Well</th>\n",
       "      <th>Metadata_JCP2022</th>\n",
       "      <th>Cells_AreaShape_Area</th>\n",
       "      <th>Cells_AreaShape_BoundingBoxArea</th>\n",
       "      <th>Cells_AreaShape_BoundingBoxMaximum_X</th>\n",
       "      <th>Cells_AreaShape_BoundingBoxMaximum_Y</th>\n",
       "      <th>Cells_AreaShape_BoundingBoxMinimum_X</th>\n",
       "      <th>Cells_AreaShape_BoundingBoxMinimum_Y</th>\n",
       "      <th>...</th>\n",
       "      <th>Nuclei_Texture_Variance_RNA_10_02_256</th>\n",
       "      <th>Nuclei_Texture_Variance_RNA_10_03_256</th>\n",
       "      <th>Nuclei_Texture_Variance_RNA_3_00_256</th>\n",
       "      <th>Nuclei_Texture_Variance_RNA_3_01_256</th>\n",
       "      <th>Nuclei_Texture_Variance_RNA_3_02_256</th>\n",
       "      <th>Nuclei_Texture_Variance_RNA_3_03_256</th>\n",
       "      <th>Nuclei_Texture_Variance_RNA_5_00_256</th>\n",
       "      <th>Nuclei_Texture_Variance_RNA_5_01_256</th>\n",
       "      <th>Nuclei_Texture_Variance_RNA_5_02_256</th>\n",
       "      <th>Nuclei_Texture_Variance_RNA_5_03_256</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>source_2</td>\n",
       "      <td>1053597806</td>\n",
       "      <td>A01</td>\n",
       "      <td>JCP2022_085227</td>\n",
       "      <td>-0.988041</td>\n",
       "      <td>-0.907001</td>\n",
       "      <td>0.096069</td>\n",
       "      <td>0.323007</td>\n",
       "      <td>0.146602</td>\n",
       "      <td>0.534867</td>\n",
       "      <td>...</td>\n",
       "      <td>1.605010</td>\n",
       "      <td>1.693312</td>\n",
       "      <td>1.615753</td>\n",
       "      <td>1.604152</td>\n",
       "      <td>1.624943</td>\n",
       "      <td>1.612151</td>\n",
       "      <td>1.589302</td>\n",
       "      <td>1.594195</td>\n",
       "      <td>1.627130</td>\n",
       "      <td>1.610461</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>source_2</td>\n",
       "      <td>1053597806</td>\n",
       "      <td>K22</td>\n",
       "      <td>JCP2022_049123</td>\n",
       "      <td>-0.247098</td>\n",
       "      <td>-0.389633</td>\n",
       "      <td>-0.828097</td>\n",
       "      <td>0.727857</td>\n",
       "      <td>-0.708414</td>\n",
       "      <td>0.887224</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.696735</td>\n",
       "      <td>-0.547206</td>\n",
       "      <td>-0.737023</td>\n",
       "      <td>-0.739017</td>\n",
       "      <td>-0.741798</td>\n",
       "      <td>-0.741577</td>\n",
       "      <td>-0.724849</td>\n",
       "      <td>-0.714124</td>\n",
       "      <td>-0.755699</td>\n",
       "      <td>-0.729048</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>source_2</td>\n",
       "      <td>1053597806</td>\n",
       "      <td>K21</td>\n",
       "      <td>JCP2022_025146</td>\n",
       "      <td>0.882814</td>\n",
       "      <td>0.635229</td>\n",
       "      <td>-0.866758</td>\n",
       "      <td>1.593473</td>\n",
       "      <td>-0.798442</td>\n",
       "      <td>1.682966</td>\n",
       "      <td>...</td>\n",
       "      <td>0.427341</td>\n",
       "      <td>0.699385</td>\n",
       "      <td>0.506531</td>\n",
       "      <td>0.478770</td>\n",
       "      <td>0.518382</td>\n",
       "      <td>0.476467</td>\n",
       "      <td>0.454404</td>\n",
       "      <td>0.473200</td>\n",
       "      <td>0.500973</td>\n",
       "      <td>0.484033</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>source_2</td>\n",
       "      <td>1053597806</td>\n",
       "      <td>K20</td>\n",
       "      <td>JCP2022_109006</td>\n",
       "      <td>1.551945</td>\n",
       "      <td>1.409719</td>\n",
       "      <td>-0.624934</td>\n",
       "      <td>-1.552434</td>\n",
       "      <td>-0.634504</td>\n",
       "      <td>-1.846982</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.016852</td>\n",
       "      <td>0.321772</td>\n",
       "      <td>0.019403</td>\n",
       "      <td>-0.023218</td>\n",
       "      <td>0.025426</td>\n",
       "      <td>-0.020011</td>\n",
       "      <td>-0.036913</td>\n",
       "      <td>-0.064012</td>\n",
       "      <td>-0.037481</td>\n",
       "      <td>-0.048811</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>source_2</td>\n",
       "      <td>1053597806</td>\n",
       "      <td>K19</td>\n",
       "      <td>JCP2022_040739</td>\n",
       "      <td>0.782228</td>\n",
       "      <td>0.394115</td>\n",
       "      <td>0.016284</td>\n",
       "      <td>0.335031</td>\n",
       "      <td>0.009199</td>\n",
       "      <td>0.228013</td>\n",
       "      <td>...</td>\n",
       "      <td>0.549137</td>\n",
       "      <td>0.589808</td>\n",
       "      <td>0.643868</td>\n",
       "      <td>0.616816</td>\n",
       "      <td>0.655204</td>\n",
       "      <td>0.615139</td>\n",
       "      <td>0.594326</td>\n",
       "      <td>0.588221</td>\n",
       "      <td>0.632808</td>\n",
       "      <td>0.615094</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>803848</th>\n",
       "      <td>source_1</td>\n",
       "      <td>UL001799</td>\n",
       "      <td>E28</td>\n",
       "      <td>JCP2022_113764</td>\n",
       "      <td>0.604395</td>\n",
       "      <td>0.369966</td>\n",
       "      <td>0.079747</td>\n",
       "      <td>-1.430108</td>\n",
       "      <td>0.084427</td>\n",
       "      <td>-1.370574</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.568779</td>\n",
       "      <td>-0.627040</td>\n",
       "      <td>-0.692929</td>\n",
       "      <td>-0.761466</td>\n",
       "      <td>-0.735498</td>\n",
       "      <td>-0.730493</td>\n",
       "      <td>-0.723268</td>\n",
       "      <td>-0.689246</td>\n",
       "      <td>-0.753452</td>\n",
       "      <td>-0.735510</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>803849</th>\n",
       "      <td>source_1</td>\n",
       "      <td>UL001799</td>\n",
       "      <td>E27</td>\n",
       "      <td>JCP2022_005165</td>\n",
       "      <td>-0.337308</td>\n",
       "      <td>-0.179527</td>\n",
       "      <td>-0.589389</td>\n",
       "      <td>-1.586146</td>\n",
       "      <td>-0.523829</td>\n",
       "      <td>-1.452674</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.942051</td>\n",
       "      <td>-0.893310</td>\n",
       "      <td>-1.033766</td>\n",
       "      <td>-1.077996</td>\n",
       "      <td>-1.055936</td>\n",
       "      <td>-1.042059</td>\n",
       "      <td>-1.028724</td>\n",
       "      <td>-0.999373</td>\n",
       "      <td>-1.056726</td>\n",
       "      <td>-1.003945</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>803850</th>\n",
       "      <td>source_1</td>\n",
       "      <td>UL001799</td>\n",
       "      <td>E26</td>\n",
       "      <td>JCP2022_051483</td>\n",
       "      <td>-0.292228</td>\n",
       "      <td>-0.463995</td>\n",
       "      <td>0.929566</td>\n",
       "      <td>0.850108</td>\n",
       "      <td>1.035715</td>\n",
       "      <td>0.820275</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.542843</td>\n",
       "      <td>-0.556913</td>\n",
       "      <td>-0.597007</td>\n",
       "      <td>-0.645565</td>\n",
       "      <td>-0.606680</td>\n",
       "      <td>-0.628779</td>\n",
       "      <td>-0.611744</td>\n",
       "      <td>-0.611571</td>\n",
       "      <td>-0.648432</td>\n",
       "      <td>-0.631909</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>803851</th>\n",
       "      <td>source_1</td>\n",
       "      <td>UL001799</td>\n",
       "      <td>E35</td>\n",
       "      <td>JCP2022_042924</td>\n",
       "      <td>0.080451</td>\n",
       "      <td>0.101718</td>\n",
       "      <td>0.480523</td>\n",
       "      <td>-1.644516</td>\n",
       "      <td>0.439748</td>\n",
       "      <td>-1.469025</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.204452</td>\n",
       "      <td>-0.115495</td>\n",
       "      <td>-0.218607</td>\n",
       "      <td>-0.260423</td>\n",
       "      <td>-0.242490</td>\n",
       "      <td>-0.273611</td>\n",
       "      <td>-0.263938</td>\n",
       "      <td>-0.233076</td>\n",
       "      <td>-0.275965</td>\n",
       "      <td>-0.253517</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>803852</th>\n",
       "      <td>source_1</td>\n",
       "      <td>UL001799</td>\n",
       "      <td>C03</td>\n",
       "      <td>JCP2022_025848</td>\n",
       "      <td>0.163948</td>\n",
       "      <td>0.670563</td>\n",
       "      <td>-0.751337</td>\n",
       "      <td>0.413076</td>\n",
       "      <td>-0.812000</td>\n",
       "      <td>0.378351</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.639439</td>\n",
       "      <td>-0.705759</td>\n",
       "      <td>-0.730660</td>\n",
       "      <td>-0.746096</td>\n",
       "      <td>-0.771677</td>\n",
       "      <td>-0.765681</td>\n",
       "      <td>-0.719094</td>\n",
       "      <td>-0.677973</td>\n",
       "      <td>-0.762016</td>\n",
       "      <td>-0.712435</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>803853 rows × 3184 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       Metadata_Source Metadata_Plate Metadata_Well Metadata_JCP2022  \\\n",
       "0             source_2     1053597806           A01   JCP2022_085227   \n",
       "1             source_2     1053597806           K22   JCP2022_049123   \n",
       "2             source_2     1053597806           K21   JCP2022_025146   \n",
       "3             source_2     1053597806           K20   JCP2022_109006   \n",
       "4             source_2     1053597806           K19   JCP2022_040739   \n",
       "...                ...            ...           ...              ...   \n",
       "803848        source_1       UL001799           E28   JCP2022_113764   \n",
       "803849        source_1       UL001799           E27   JCP2022_005165   \n",
       "803850        source_1       UL001799           E26   JCP2022_051483   \n",
       "803851        source_1       UL001799           E35   JCP2022_042924   \n",
       "803852        source_1       UL001799           C03   JCP2022_025848   \n",
       "\n",
       "        Cells_AreaShape_Area  Cells_AreaShape_BoundingBoxArea  \\\n",
       "0                  -0.988041                        -0.907001   \n",
       "1                  -0.247098                        -0.389633   \n",
       "2                   0.882814                         0.635229   \n",
       "3                   1.551945                         1.409719   \n",
       "4                   0.782228                         0.394115   \n",
       "...                      ...                              ...   \n",
       "803848              0.604395                         0.369966   \n",
       "803849             -0.337308                        -0.179527   \n",
       "803850             -0.292228                        -0.463995   \n",
       "803851              0.080451                         0.101718   \n",
       "803852              0.163948                         0.670563   \n",
       "\n",
       "        Cells_AreaShape_BoundingBoxMaximum_X  \\\n",
       "0                                   0.096069   \n",
       "1                                  -0.828097   \n",
       "2                                  -0.866758   \n",
       "3                                  -0.624934   \n",
       "4                                   0.016284   \n",
       "...                                      ...   \n",
       "803848                              0.079747   \n",
       "803849                             -0.589389   \n",
       "803850                              0.929566   \n",
       "803851                              0.480523   \n",
       "803852                             -0.751337   \n",
       "\n",
       "        Cells_AreaShape_BoundingBoxMaximum_Y  \\\n",
       "0                                   0.323007   \n",
       "1                                   0.727857   \n",
       "2                                   1.593473   \n",
       "3                                  -1.552434   \n",
       "4                                   0.335031   \n",
       "...                                      ...   \n",
       "803848                             -1.430108   \n",
       "803849                             -1.586146   \n",
       "803850                              0.850108   \n",
       "803851                             -1.644516   \n",
       "803852                              0.413076   \n",
       "\n",
       "        Cells_AreaShape_BoundingBoxMinimum_X  \\\n",
       "0                                   0.146602   \n",
       "1                                  -0.708414   \n",
       "2                                  -0.798442   \n",
       "3                                  -0.634504   \n",
       "4                                   0.009199   \n",
       "...                                      ...   \n",
       "803848                              0.084427   \n",
       "803849                             -0.523829   \n",
       "803850                              1.035715   \n",
       "803851                              0.439748   \n",
       "803852                             -0.812000   \n",
       "\n",
       "        Cells_AreaShape_BoundingBoxMinimum_Y  ...  \\\n",
       "0                                   0.534867  ...   \n",
       "1                                   0.887224  ...   \n",
       "2                                   1.682966  ...   \n",
       "3                                  -1.846982  ...   \n",
       "4                                   0.228013  ...   \n",
       "...                                      ...  ...   \n",
       "803848                             -1.370574  ...   \n",
       "803849                             -1.452674  ...   \n",
       "803850                              0.820275  ...   \n",
       "803851                             -1.469025  ...   \n",
       "803852                              0.378351  ...   \n",
       "\n",
       "        Nuclei_Texture_Variance_RNA_10_02_256  \\\n",
       "0                                    1.605010   \n",
       "1                                   -0.696735   \n",
       "2                                    0.427341   \n",
       "3                                   -0.016852   \n",
       "4                                    0.549137   \n",
       "...                                       ...   \n",
       "803848                              -0.568779   \n",
       "803849                              -0.942051   \n",
       "803850                              -0.542843   \n",
       "803851                              -0.204452   \n",
       "803852                              -0.639439   \n",
       "\n",
       "        Nuclei_Texture_Variance_RNA_10_03_256  \\\n",
       "0                                    1.693312   \n",
       "1                                   -0.547206   \n",
       "2                                    0.699385   \n",
       "3                                    0.321772   \n",
       "4                                    0.589808   \n",
       "...                                       ...   \n",
       "803848                              -0.627040   \n",
       "803849                              -0.893310   \n",
       "803850                              -0.556913   \n",
       "803851                              -0.115495   \n",
       "803852                              -0.705759   \n",
       "\n",
       "        Nuclei_Texture_Variance_RNA_3_00_256  \\\n",
       "0                                   1.615753   \n",
       "1                                  -0.737023   \n",
       "2                                   0.506531   \n",
       "3                                   0.019403   \n",
       "4                                   0.643868   \n",
       "...                                      ...   \n",
       "803848                             -0.692929   \n",
       "803849                             -1.033766   \n",
       "803850                             -0.597007   \n",
       "803851                             -0.218607   \n",
       "803852                             -0.730660   \n",
       "\n",
       "        Nuclei_Texture_Variance_RNA_3_01_256  \\\n",
       "0                                   1.604152   \n",
       "1                                  -0.739017   \n",
       "2                                   0.478770   \n",
       "3                                  -0.023218   \n",
       "4                                   0.616816   \n",
       "...                                      ...   \n",
       "803848                             -0.761466   \n",
       "803849                             -1.077996   \n",
       "803850                             -0.645565   \n",
       "803851                             -0.260423   \n",
       "803852                             -0.746096   \n",
       "\n",
       "        Nuclei_Texture_Variance_RNA_3_02_256  \\\n",
       "0                                   1.624943   \n",
       "1                                  -0.741798   \n",
       "2                                   0.518382   \n",
       "3                                   0.025426   \n",
       "4                                   0.655204   \n",
       "...                                      ...   \n",
       "803848                             -0.735498   \n",
       "803849                             -1.055936   \n",
       "803850                             -0.606680   \n",
       "803851                             -0.242490   \n",
       "803852                             -0.771677   \n",
       "\n",
       "        Nuclei_Texture_Variance_RNA_3_03_256  \\\n",
       "0                                   1.612151   \n",
       "1                                  -0.741577   \n",
       "2                                   0.476467   \n",
       "3                                  -0.020011   \n",
       "4                                   0.615139   \n",
       "...                                      ...   \n",
       "803848                             -0.730493   \n",
       "803849                             -1.042059   \n",
       "803850                             -0.628779   \n",
       "803851                             -0.273611   \n",
       "803852                             -0.765681   \n",
       "\n",
       "        Nuclei_Texture_Variance_RNA_5_00_256  \\\n",
       "0                                   1.589302   \n",
       "1                                  -0.724849   \n",
       "2                                   0.454404   \n",
       "3                                  -0.036913   \n",
       "4                                   0.594326   \n",
       "...                                      ...   \n",
       "803848                             -0.723268   \n",
       "803849                             -1.028724   \n",
       "803850                             -0.611744   \n",
       "803851                             -0.263938   \n",
       "803852                             -0.719094   \n",
       "\n",
       "        Nuclei_Texture_Variance_RNA_5_01_256  \\\n",
       "0                                   1.594195   \n",
       "1                                  -0.714124   \n",
       "2                                   0.473200   \n",
       "3                                  -0.064012   \n",
       "4                                   0.588221   \n",
       "...                                      ...   \n",
       "803848                             -0.689246   \n",
       "803849                             -0.999373   \n",
       "803850                             -0.611571   \n",
       "803851                             -0.233076   \n",
       "803852                             -0.677973   \n",
       "\n",
       "        Nuclei_Texture_Variance_RNA_5_02_256  \\\n",
       "0                                   1.627130   \n",
       "1                                  -0.755699   \n",
       "2                                   0.500973   \n",
       "3                                  -0.037481   \n",
       "4                                   0.632808   \n",
       "...                                      ...   \n",
       "803848                             -0.753452   \n",
       "803849                             -1.056726   \n",
       "803850                             -0.648432   \n",
       "803851                             -0.275965   \n",
       "803852                             -0.762016   \n",
       "\n",
       "        Nuclei_Texture_Variance_RNA_5_03_256  \n",
       "0                                   1.610461  \n",
       "1                                  -0.729048  \n",
       "2                                   0.484033  \n",
       "3                                  -0.048811  \n",
       "4                                   0.615094  \n",
       "...                                      ...  \n",
       "803848                             -0.735510  \n",
       "803849                             -1.003945  \n",
       "803850                             -0.631909  \n",
       "803851                             -0.253517  \n",
       "803852                             -0.712435  \n",
       "\n",
       "[803853 rows x 3184 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pd.read_parquet(path/\"data/profiles_var_mad_int.parquet\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "dec58da8a37f417fa7399dae94ffcf23",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "Resolving data files:   0%|          | 0/3388 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "from datasets import load_dataset\n",
    "drug_metadata =  load_dataset(\"tahoebio/Tahoe-100M\",\"drug_metadata\", split=\"train\")\n",
    "drug_metadata = drug_metadata.to_pandas()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>drug</th>\n",
       "      <th>targets</th>\n",
       "      <th>moa-broad</th>\n",
       "      <th>moa-fine</th>\n",
       "      <th>human-approved</th>\n",
       "      <th>clinical-trials</th>\n",
       "      <th>gpt-notes-approval</th>\n",
       "      <th>canonical_smiles</th>\n",
       "      <th>pubchem_cid</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Talc</td>\n",
       "      <td>None</td>\n",
       "      <td>unclear</td>\n",
       "      <td>unclear</td>\n",
       "      <td>yes</td>\n",
       "      <td>yes</td>\n",
       "      <td>Talc used in pharma and cosmetics; safety unde...</td>\n",
       "      <td>[OH-].[OH-].[O-][Si]12O[Si]3(O[Si](O1)(O[Si](O...</td>\n",
       "      <td>165411828.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Bortezomib</td>\n",
       "      <td>PSMB5</td>\n",
       "      <td>inhibitor/antagonist</td>\n",
       "      <td>Proteasome inhibitor</td>\n",
       "      <td>yes</td>\n",
       "      <td>yes</td>\n",
       "      <td>Approved for multiple myeloma and mantle cell ...</td>\n",
       "      <td>B(C(CC(C)C)NC(=O)C(CC1=CC=CC=C1)NC(=O)C2=NC=CN...</td>\n",
       "      <td>387447.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Ixazomib</td>\n",
       "      <td>PSMB5</td>\n",
       "      <td>inhibitor/antagonist</td>\n",
       "      <td>Proteasome inhibitor</td>\n",
       "      <td>yes</td>\n",
       "      <td>yes</td>\n",
       "      <td>Approved for multiple myeloma treatment.</td>\n",
       "      <td>B(C(CC(C)C)NC(=O)CNC(=O)C1=C(C=CC(=C1)Cl)Cl)(O)O</td>\n",
       "      <td>25183872.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Ixazomib citrate</td>\n",
       "      <td>PSMB1, PSMB2, PSMB5</td>\n",
       "      <td>inhibitor/antagonist</td>\n",
       "      <td>Proteasome inhibitor</td>\n",
       "      <td>yes</td>\n",
       "      <td>yes</td>\n",
       "      <td>Approved for multiple myeloma treatment as par...</td>\n",
       "      <td>B1(OC(=O)C(O1)(CC(=O)O)CC(=O)O)C(CC(C)C)NC(=O)...</td>\n",
       "      <td>56844015.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Lactate (calcium)</td>\n",
       "      <td>None</td>\n",
       "      <td>unclear</td>\n",
       "      <td>unclear</td>\n",
       "      <td>yes</td>\n",
       "      <td>yes</td>\n",
       "      <td>Used in medical settings, but not specifically...</td>\n",
       "      <td>C.CC(C(=O)[O-])O.[Ca+2]</td>\n",
       "      <td>168311648.0</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>374</th>\n",
       "      <td>Verteporfin</td>\n",
       "      <td>YAP1</td>\n",
       "      <td>inhibitor/antagonist</td>\n",
       "      <td>unclear</td>\n",
       "      <td>yes</td>\n",
       "      <td>yes</td>\n",
       "      <td>Used in photodynamic therapy for macular degen...</td>\n",
       "      <td>None</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>375</th>\n",
       "      <td>Quinidine (15% dihydroquinidine)</td>\n",
       "      <td>KCNH2</td>\n",
       "      <td>inhibitor/antagonist</td>\n",
       "      <td>unclear</td>\n",
       "      <td>yes</td>\n",
       "      <td>yes</td>\n",
       "      <td>Approved for arrhythmias as part of quinine al...</td>\n",
       "      <td>COC1=CC2=C(C=CN=C2C=C1)[C@@H]([C@H]3C[C@@H]4CC...</td>\n",
       "      <td>441074.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>376</th>\n",
       "      <td>Canagliflozin (hemihydrate)</td>\n",
       "      <td>SLC5A2</td>\n",
       "      <td>inhibitor/antagonist</td>\n",
       "      <td>Glucose transporter inhibitor</td>\n",
       "      <td>yes</td>\n",
       "      <td>yes</td>\n",
       "      <td>Approved for type 2 diabetes.</td>\n",
       "      <td>CC1=C(C=C(C=C1)[C@H]2[C@@H]([C@H]([C@@H]([C@H]...</td>\n",
       "      <td>24997615.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>377</th>\n",
       "      <td>Osimertinib (mesylate)</td>\n",
       "      <td>EGFR</td>\n",
       "      <td>inhibitor/antagonist</td>\n",
       "      <td>EGFR/ERBB inhibitor</td>\n",
       "      <td>yes</td>\n",
       "      <td>yes</td>\n",
       "      <td>Approved for non-small cell lung cancer treatm...</td>\n",
       "      <td>CN1C=C(C2=CC=CC=C21)C3=NC(=NC=C3)NC4=C(C=C(C(=...</td>\n",
       "      <td>78357807.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>378</th>\n",
       "      <td>γ-Oryzanol</td>\n",
       "      <td>None</td>\n",
       "      <td>inhibitor/antagonist</td>\n",
       "      <td>DNA methyltransferase inhibitor</td>\n",
       "      <td>no</td>\n",
       "      <td>yes</td>\n",
       "      <td>Used in supplements; limited human data.</td>\n",
       "      <td>C[C@H](CCC=C(C)C)[C@H]1CC[C@@]2([C@@]1(CC[C@]3...</td>\n",
       "      <td>5282164.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>379 rows × 9 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                 drug              targets  \\\n",
       "0                                Talc                 None   \n",
       "1                          Bortezomib                PSMB5   \n",
       "2                            Ixazomib                PSMB5   \n",
       "3                    Ixazomib citrate  PSMB1, PSMB2, PSMB5   \n",
       "4                   Lactate (calcium)                 None   \n",
       "..                                ...                  ...   \n",
       "374                       Verteporfin                 YAP1   \n",
       "375  Quinidine (15% dihydroquinidine)                KCNH2   \n",
       "376       Canagliflozin (hemihydrate)               SLC5A2   \n",
       "377            Osimertinib (mesylate)                 EGFR   \n",
       "378                        γ-Oryzanol                 None   \n",
       "\n",
       "                moa-broad                         moa-fine human-approved  \\\n",
       "0                 unclear                          unclear            yes   \n",
       "1    inhibitor/antagonist             Proteasome inhibitor            yes   \n",
       "2    inhibitor/antagonist             Proteasome inhibitor            yes   \n",
       "3    inhibitor/antagonist             Proteasome inhibitor            yes   \n",
       "4                 unclear                          unclear            yes   \n",
       "..                    ...                              ...            ...   \n",
       "374  inhibitor/antagonist                          unclear            yes   \n",
       "375  inhibitor/antagonist                          unclear            yes   \n",
       "376  inhibitor/antagonist    Glucose transporter inhibitor            yes   \n",
       "377  inhibitor/antagonist              EGFR/ERBB inhibitor            yes   \n",
       "378  inhibitor/antagonist  DNA methyltransferase inhibitor             no   \n",
       "\n",
       "    clinical-trials                                 gpt-notes-approval  \\\n",
       "0               yes  Talc used in pharma and cosmetics; safety unde...   \n",
       "1               yes  Approved for multiple myeloma and mantle cell ...   \n",
       "2               yes           Approved for multiple myeloma treatment.   \n",
       "3               yes  Approved for multiple myeloma treatment as par...   \n",
       "4               yes  Used in medical settings, but not specifically...   \n",
       "..              ...                                                ...   \n",
       "374             yes  Used in photodynamic therapy for macular degen...   \n",
       "375             yes  Approved for arrhythmias as part of quinine al...   \n",
       "376             yes                      Approved for type 2 diabetes.   \n",
       "377             yes  Approved for non-small cell lung cancer treatm...   \n",
       "378             yes           Used in supplements; limited human data.   \n",
       "\n",
       "                                      canonical_smiles  pubchem_cid  \n",
       "0    [OH-].[OH-].[O-][Si]12O[Si]3(O[Si](O1)(O[Si](O...  165411828.0  \n",
       "1    B(C(CC(C)C)NC(=O)C(CC1=CC=CC=C1)NC(=O)C2=NC=CN...     387447.0  \n",
       "2     B(C(CC(C)C)NC(=O)CNC(=O)C1=C(C=CC(=C1)Cl)Cl)(O)O   25183872.0  \n",
       "3    B1(OC(=O)C(O1)(CC(=O)O)CC(=O)O)C(CC(C)C)NC(=O)...   56844015.0  \n",
       "4                              C.CC(C(=O)[O-])O.[Ca+2]  168311648.0  \n",
       "..                                                 ...          ...  \n",
       "374                                               None          NaN  \n",
       "375  COC1=CC2=C(C=CN=C2C=C1)[C@@H]([C@H]3C[C@@H]4CC...     441074.0  \n",
       "376  CC1=C(C=C(C=C1)[C@H]2[C@@H]([C@H]([C@@H]([C@H]...   24997615.0  \n",
       "377  CN1C=C(C2=CC=CC=C21)C3=NC(=NC=C3)NC4=C(C=C(C(=...   78357807.0  \n",
       "378  C[C@H](CCC=C(C)C)[C@H]1CC[C@@]2([C@@]1(CC[C@]3...    5282164.0  \n",
       "\n",
       "[379 rows x 9 columns]"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "drug_metadata.to_pandas()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 53,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pubchempy as pcp\n",
    "import time\n",
    "\n",
    "def get_compounds(inchikey, sleep_sec=0.3):\n",
    "    \"\"\"\n",
    "    Get compound synonyms from an InChIKey using PubChemPy.\n",
    "    \n",
    "    Args:\n",
    "        inchikey (str): InChIKey of the compound\n",
    "        sleep_sec (float): Seconds to sleep to avoid rate limiting\n",
    "        \n",
    "    Returns:\n",
    "        list: List of synonyms (empty if error or none found)\n",
    "    \"\"\"\n",
    "    try:\n",
    "        # Get compound from InChIKey\n",
    "        compounds = pcp.get_compounds(inchikey, 'inchikey')\n",
    "        if not compounds:\n",
    "            return []\n",
    "        \n",
    "        # Sleep to avoid rate limiting\n",
    "        time.sleep(sleep_sec)\n",
    "        return compounds\n",
    "        \n",
    "        # # Get synonyms using CID\n",
    "        # synonyms_data = pcp.get_synonyms(cid, 'cid')\n",
    "        # if not synonyms_data:\n",
    "        #     return compounds[0].synonyms or []\n",
    "            \n",
    "        # # Return synonyms list\n",
    "        # return compounds synonyms_data[0].get('Synonym', [])\n",
    "        \n",
    "    except Exception as e:\n",
    "        print(f\"Error for {inchikey}: {e}\")\n",
    "        return None\n",
    "\n",
    "# Example usage\n",
    "inchikey = {}\n",
    "for k in sim_df.InChIKey.unique():\n",
    "    compounds = get_compounds(k)\n",
    "    if len(compounds) > 0:\n",
    "        inchikey[k] = compounds\n",
    "\n",
    "# synonyms = get_synonyms(inchikey)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 90,
   "metadata": {},
   "outputs": [],
   "source": [
    "chemid_dict = {}\n",
    "for k,v in inchikey.items():\n",
    "    for c in v:\n",
    "        chemid_dict[c.cid] = k\n",
    "\n",
    "import numpy as np\n",
    "pubchem_id_tahoe = drug_metadata[\"pubchem_cid\"].values.tolist()\n",
    "pubchem_id_jump = list(chemid_dict.keys())\n",
    "chemid_dict = {k:v for k,v in chemid_dict.items() if k in pubchem_id_tahoe}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 98,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_inchi_pubmed_id = pd.DataFrame(chemid_dict, index=[\"InChIKey\"]).T.reset_index()\n",
    "df_inchi_pubmed_id.columns = [\"pubchem_cid\", \"InChIKey\", ]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 100,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>drug</th>\n",
       "      <th>targets</th>\n",
       "      <th>moa-broad</th>\n",
       "      <th>moa-fine</th>\n",
       "      <th>human-approved</th>\n",
       "      <th>clinical-trials</th>\n",
       "      <th>gpt-notes-approval</th>\n",
       "      <th>canonical_smiles</th>\n",
       "      <th>pubchem_cid</th>\n",
       "      <th>InChIKey</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Talc</td>\n",
       "      <td>None</td>\n",
       "      <td>unclear</td>\n",
       "      <td>unclear</td>\n",
       "      <td>yes</td>\n",
       "      <td>yes</td>\n",
       "      <td>Talc used in pharma and cosmetics; safety unde...</td>\n",
       "      <td>[OH-].[OH-].[O-][Si]12O[Si]3(O[Si](O1)(O[Si](O...</td>\n",
       "      <td>165411828.0</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Bortezomib</td>\n",
       "      <td>PSMB5</td>\n",
       "      <td>inhibitor/antagonist</td>\n",
       "      <td>Proteasome inhibitor</td>\n",
       "      <td>yes</td>\n",
       "      <td>yes</td>\n",
       "      <td>Approved for multiple myeloma and mantle cell ...</td>\n",
       "      <td>B(C(CC(C)C)NC(=O)C(CC1=CC=CC=C1)NC(=O)C2=NC=CN...</td>\n",
       "      <td>387447.0</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Ixazomib</td>\n",
       "      <td>PSMB5</td>\n",
       "      <td>inhibitor/antagonist</td>\n",
       "      <td>Proteasome inhibitor</td>\n",
       "      <td>yes</td>\n",
       "      <td>yes</td>\n",
       "      <td>Approved for multiple myeloma treatment.</td>\n",
       "      <td>B(C(CC(C)C)NC(=O)CNC(=O)C1=C(C=CC(=C1)Cl)Cl)(O)O</td>\n",
       "      <td>25183872.0</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Ixazomib citrate</td>\n",
       "      <td>PSMB1, PSMB2, PSMB5</td>\n",
       "      <td>inhibitor/antagonist</td>\n",
       "      <td>Proteasome inhibitor</td>\n",
       "      <td>yes</td>\n",
       "      <td>yes</td>\n",
       "      <td>Approved for multiple myeloma treatment as par...</td>\n",
       "      <td>B1(OC(=O)C(O1)(CC(=O)O)CC(=O)O)C(CC(C)C)NC(=O)...</td>\n",
       "      <td>56844015.0</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Lactate (calcium)</td>\n",
       "      <td>None</td>\n",
       "      <td>unclear</td>\n",
       "      <td>unclear</td>\n",
       "      <td>yes</td>\n",
       "      <td>yes</td>\n",
       "      <td>Used in medical settings, but not specifically...</td>\n",
       "      <td>C.CC(C(=O)[O-])O.[Ca+2]</td>\n",
       "      <td>168311648.0</td>\n",
       "      <td>NaN</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>374</th>\n",
       "      <td>Verteporfin</td>\n",
       "      <td>YAP1</td>\n",
       "      <td>inhibitor/antagonist</td>\n",
       "      <td>unclear</td>\n",
       "      <td>yes</td>\n",
       "      <td>yes</td>\n",
       "      <td>Used in photodynamic therapy for macular degen...</td>\n",
       "      <td>None</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>375</th>\n",
       "      <td>Quinidine (15% dihydroquinidine)</td>\n",
       "      <td>KCNH2</td>\n",
       "      <td>inhibitor/antagonist</td>\n",
       "      <td>unclear</td>\n",
       "      <td>yes</td>\n",
       "      <td>yes</td>\n",
       "      <td>Approved for arrhythmias as part of quinine al...</td>\n",
       "      <td>COC1=CC2=C(C=CN=C2C=C1)[C@@H]([C@H]3C[C@@H]4CC...</td>\n",
       "      <td>441074.0</td>\n",
       "      <td>LOUPRKONTZGTKE-LHHVKLHASA-N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>376</th>\n",
       "      <td>Canagliflozin (hemihydrate)</td>\n",
       "      <td>SLC5A2</td>\n",
       "      <td>inhibitor/antagonist</td>\n",
       "      <td>Glucose transporter inhibitor</td>\n",
       "      <td>yes</td>\n",
       "      <td>yes</td>\n",
       "      <td>Approved for type 2 diabetes.</td>\n",
       "      <td>CC1=C(C=C(C=C1)[C@H]2[C@@H]([C@H]([C@@H]([C@H]...</td>\n",
       "      <td>24997615.0</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>377</th>\n",
       "      <td>Osimertinib (mesylate)</td>\n",
       "      <td>EGFR</td>\n",
       "      <td>inhibitor/antagonist</td>\n",
       "      <td>EGFR/ERBB inhibitor</td>\n",
       "      <td>yes</td>\n",
       "      <td>yes</td>\n",
       "      <td>Approved for non-small cell lung cancer treatm...</td>\n",
       "      <td>CN1C=C(C2=CC=CC=C21)C3=NC(=NC=C3)NC4=C(C=C(C(=...</td>\n",
       "      <td>78357807.0</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>378</th>\n",
       "      <td>γ-Oryzanol</td>\n",
       "      <td>None</td>\n",
       "      <td>inhibitor/antagonist</td>\n",
       "      <td>DNA methyltransferase inhibitor</td>\n",
       "      <td>no</td>\n",
       "      <td>yes</td>\n",
       "      <td>Used in supplements; limited human data.</td>\n",
       "      <td>C[C@H](CCC=C(C)C)[C@H]1CC[C@@]2([C@@]1(CC[C@]3...</td>\n",
       "      <td>5282164.0</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>379 rows × 10 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                 drug              targets  \\\n",
       "0                                Talc                 None   \n",
       "1                          Bortezomib                PSMB5   \n",
       "2                            Ixazomib                PSMB5   \n",
       "3                    Ixazomib citrate  PSMB1, PSMB2, PSMB5   \n",
       "4                   Lactate (calcium)                 None   \n",
       "..                                ...                  ...   \n",
       "374                       Verteporfin                 YAP1   \n",
       "375  Quinidine (15% dihydroquinidine)                KCNH2   \n",
       "376       Canagliflozin (hemihydrate)               SLC5A2   \n",
       "377            Osimertinib (mesylate)                 EGFR   \n",
       "378                        γ-Oryzanol                 None   \n",
       "\n",
       "                moa-broad                         moa-fine human-approved  \\\n",
       "0                 unclear                          unclear            yes   \n",
       "1    inhibitor/antagonist             Proteasome inhibitor            yes   \n",
       "2    inhibitor/antagonist             Proteasome inhibitor            yes   \n",
       "3    inhibitor/antagonist             Proteasome inhibitor            yes   \n",
       "4                 unclear                          unclear            yes   \n",
       "..                    ...                              ...            ...   \n",
       "374  inhibitor/antagonist                          unclear            yes   \n",
       "375  inhibitor/antagonist                          unclear            yes   \n",
       "376  inhibitor/antagonist    Glucose transporter inhibitor            yes   \n",
       "377  inhibitor/antagonist              EGFR/ERBB inhibitor            yes   \n",
       "378  inhibitor/antagonist  DNA methyltransferase inhibitor             no   \n",
       "\n",
       "    clinical-trials                                 gpt-notes-approval  \\\n",
       "0               yes  Talc used in pharma and cosmetics; safety unde...   \n",
       "1               yes  Approved for multiple myeloma and mantle cell ...   \n",
       "2               yes           Approved for multiple myeloma treatment.   \n",
       "3               yes  Approved for multiple myeloma treatment as par...   \n",
       "4               yes  Used in medical settings, but not specifically...   \n",
       "..              ...                                                ...   \n",
       "374             yes  Used in photodynamic therapy for macular degen...   \n",
       "375             yes  Approved for arrhythmias as part of quinine al...   \n",
       "376             yes                      Approved for type 2 diabetes.   \n",
       "377             yes  Approved for non-small cell lung cancer treatm...   \n",
       "378             yes           Used in supplements; limited human data.   \n",
       "\n",
       "                                      canonical_smiles  pubchem_cid  \\\n",
       "0    [OH-].[OH-].[O-][Si]12O[Si]3(O[Si](O1)(O[Si](O...  165411828.0   \n",
       "1    B(C(CC(C)C)NC(=O)C(CC1=CC=CC=C1)NC(=O)C2=NC=CN...     387447.0   \n",
       "2     B(C(CC(C)C)NC(=O)CNC(=O)C1=C(C=CC(=C1)Cl)Cl)(O)O   25183872.0   \n",
       "3    B1(OC(=O)C(O1)(CC(=O)O)CC(=O)O)C(CC(C)C)NC(=O)...   56844015.0   \n",
       "4                              C.CC(C(=O)[O-])O.[Ca+2]  168311648.0   \n",
       "..                                                 ...          ...   \n",
       "374                                               None          NaN   \n",
       "375  COC1=CC2=C(C=CN=C2C=C1)[C@@H]([C@H]3C[C@@H]4CC...     441074.0   \n",
       "376  CC1=C(C=C(C=C1)[C@H]2[C@@H]([C@H]([C@@H]([C@H]...   24997615.0   \n",
       "377  CN1C=C(C2=CC=CC=C21)C3=NC(=NC=C3)NC4=C(C=C(C(=...   78357807.0   \n",
       "378  C[C@H](CCC=C(C)C)[C@H]1CC[C@@]2([C@@]1(CC[C@]3...    5282164.0   \n",
       "\n",
       "                        InChIKey  \n",
       "0                            NaN  \n",
       "1                            NaN  \n",
       "2                            NaN  \n",
       "3                            NaN  \n",
       "4                            NaN  \n",
       "..                           ...  \n",
       "374                          NaN  \n",
       "375  LOUPRKONTZGTKE-LHHVKLHASA-N  \n",
       "376                          NaN  \n",
       "377                          NaN  \n",
       "378                          NaN  \n",
       "\n",
       "[379 rows x 10 columns]"
      ]
     },
     "execution_count": 100,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "drug_metadata = drug_metadata.merge(\n",
    "    df_inchi_pubmed_id,\n",
    "    on=\"pubchem_cid\",\n",
    "    how=\"left\"\n",
    ")\n",
    "\n",
    "drug_metadata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>drug</th>\n",
       "      <th>InChIKey</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>36</th>\n",
       "      <td>Salicylic acid</td>\n",
       "      <td>YGSDEFSMJLZEOE-UHFFFAOYSA-N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>58</th>\n",
       "      <td>5-Azacytidine</td>\n",
       "      <td>NMUSYJAQQFHJEW-KVTDHHQDSA-N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>69</th>\n",
       "      <td>Larotrectinib</td>\n",
       "      <td>NYNZQNWKBKUAII-KBXCAEBGSA-N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>72</th>\n",
       "      <td>Filgotinib</td>\n",
       "      <td>RIJLVEAXPNLDTC-UHFFFAOYSA-N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>75</th>\n",
       "      <td>Cilostazol</td>\n",
       "      <td>RRGUKTPIGVIEKM-UHFFFAOYSA-N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>81</th>\n",
       "      <td>Lonafarnib</td>\n",
       "      <td>DHMTURDWPRKSOA-RUZDIDTESA-N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>95</th>\n",
       "      <td>Acetohexamide</td>\n",
       "      <td>VGZSUPCWNCWDAN-UHFFFAOYSA-N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>113</th>\n",
       "      <td>Homoharringtonine</td>\n",
       "      <td>HYFHYPWGAURHIV-JFIAXGOJSA-N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>169</th>\n",
       "      <td>Ponatinib</td>\n",
       "      <td>PHXJVRSECIGDHY-UHFFFAOYSA-N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>187</th>\n",
       "      <td>Nevirapine</td>\n",
       "      <td>NQDJXKOVJZTUJA-UHFFFAOYSA-N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>198</th>\n",
       "      <td>Menadione</td>\n",
       "      <td>MJVAVZPDRWSRRC-UHFFFAOYSA-N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>212</th>\n",
       "      <td>Olanzapine</td>\n",
       "      <td>KVWDHTXUZHCGIO-UHFFFAOYSA-N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>246</th>\n",
       "      <td>Dexamethasone</td>\n",
       "      <td>UREBDLICKHMUKA-CXSFZGCWSA-N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>273</th>\n",
       "      <td>Cyclosporin A</td>\n",
       "      <td>PMATZTZNYRCHOR-CGLBZJNRSA-N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>343</th>\n",
       "      <td>Regorafenib</td>\n",
       "      <td>FNHKPVJBJVTLMP-UHFFFAOYSA-N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>350</th>\n",
       "      <td>Tranilast</td>\n",
       "      <td>NZHGWWWHIYHZNX-CSKARUKUSA-N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>375</th>\n",
       "      <td>Quinidine (15% dihydroquinidine)</td>\n",
       "      <td>LOUPRKONTZGTKE-LHHVKLHASA-N</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                 drug                     InChIKey\n",
       "36                     Salicylic acid  YGSDEFSMJLZEOE-UHFFFAOYSA-N\n",
       "58                      5-Azacytidine  NMUSYJAQQFHJEW-KVTDHHQDSA-N\n",
       "69                      Larotrectinib  NYNZQNWKBKUAII-KBXCAEBGSA-N\n",
       "72                         Filgotinib  RIJLVEAXPNLDTC-UHFFFAOYSA-N\n",
       "75                         Cilostazol  RRGUKTPIGVIEKM-UHFFFAOYSA-N\n",
       "81                         Lonafarnib  DHMTURDWPRKSOA-RUZDIDTESA-N\n",
       "95                      Acetohexamide  VGZSUPCWNCWDAN-UHFFFAOYSA-N\n",
       "113                 Homoharringtonine  HYFHYPWGAURHIV-JFIAXGOJSA-N\n",
       "169                         Ponatinib  PHXJVRSECIGDHY-UHFFFAOYSA-N\n",
       "187                        Nevirapine  NQDJXKOVJZTUJA-UHFFFAOYSA-N\n",
       "198                         Menadione  MJVAVZPDRWSRRC-UHFFFAOYSA-N\n",
       "212                        Olanzapine  KVWDHTXUZHCGIO-UHFFFAOYSA-N\n",
       "246                     Dexamethasone  UREBDLICKHMUKA-CXSFZGCWSA-N\n",
       "273                     Cyclosporin A  PMATZTZNYRCHOR-CGLBZJNRSA-N\n",
       "343                       Regorafenib  FNHKPVJBJVTLMP-UHFFFAOYSA-N\n",
       "350                         Tranilast  NZHGWWWHIYHZNX-CSKARUKUSA-N\n",
       "375  Quinidine (15% dihydroquinidine)  LOUPRKONTZGTKE-LHHVKLHASA-N"
      ]
     },
     "execution_count": 36,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "drug_metadata[[\"drug\",\"InChIKey\"]].dropna()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "drug_metadata = pd.read_csv(path/\"data/drug_metadata_inchikey.csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>broad_sample</th>\n",
       "      <th>InChIKey</th>\n",
       "      <th>pert_iname</th>\n",
       "      <th>pubchem_cid</th>\n",
       "      <th>gene</th>\n",
       "      <th>pert_type</th>\n",
       "      <th>control_type</th>\n",
       "      <th>smiles</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>BRD-A86665761-001-01-1</td>\n",
       "      <td>TZDUHAJSIBHXDL-UHFFFAOYSA-N</td>\n",
       "      <td>gabapentin-enacarbil</td>\n",
       "      <td>9883933.0</td>\n",
       "      <td>CACNB4</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "      <td>CC(C)C(=O)OC(C)OC(=O)NCC1(CC(O)=O)CCCCC1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>BRD-A22032524-074-09-9</td>\n",
       "      <td>HTIQEAQVCYTUBX-UHFFFAOYSA-N</td>\n",
       "      <td>amlodipine</td>\n",
       "      <td>2162.0</td>\n",
       "      <td>CACNA2D3</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "      <td>CCOC(=O)C1=C(COCCN)NC(C)=C(C1c1ccccc1Cl)C(=O)OC</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>BRD-A01078468-001-14-8</td>\n",
       "      <td>PBBGSZCBWVPOOL-UHFFFAOYSA-N</td>\n",
       "      <td>hexestrol</td>\n",
       "      <td>3606.0</td>\n",
       "      <td>AKR1C1</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "      <td>CCC(C(CC)c1ccc(O)cc1)c1ccc(O)cc1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>BRD-K48278478-001-01-2</td>\n",
       "      <td>LOUPRKONTZGTKE-AFHBHXEDSA-N</td>\n",
       "      <td>quinine</td>\n",
       "      <td>94175.0</td>\n",
       "      <td>KCNN4</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "      <td>COc1ccc2nccc([C@@H](O)[C@H]3C[C@@H]4CC[N@]3C[C...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>BRD-K36574127-001-01-3</td>\n",
       "      <td>NYNZQNWKBKUAII-KBXCAEBGSA-N</td>\n",
       "      <td>LOXO-101</td>\n",
       "      <td>46188928.0</td>\n",
       "      <td>NTRK1</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "      <td>O[C@H]1CCN(C1)C(=O)Nc1cnn2ccc(nc12)N1CCC[C@@H]...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>302</th>\n",
       "      <td>BRD-K24616672-003-20-1</td>\n",
       "      <td>MFDFERRIHVXMIY-UHFFFAOYSA-N</td>\n",
       "      <td>procaine</td>\n",
       "      <td>4914.0</td>\n",
       "      <td>HTR3A</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "      <td>CCN(CC)CCOC(=O)c1ccc(N)cc1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>303</th>\n",
       "      <td>BRD-A82396632-008-30-8</td>\n",
       "      <td>BYBLEWFAAKGYCD-UHFFFAOYSA-N</td>\n",
       "      <td>miconazole</td>\n",
       "      <td>4189.0</td>\n",
       "      <td>KCNN1</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Clc1ccc(COC(Cn2ccnc2)c2ccc(Cl)cc2Cl)c(Cl)c1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>304</th>\n",
       "      <td>BRD-K61250553-003-30-6</td>\n",
       "      <td>RDOIQAHITMMDAJ-UHFFFAOYSA-N</td>\n",
       "      <td>loperamide</td>\n",
       "      <td>3955.0</td>\n",
       "      <td>OPRM1</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "      <td>CN(C)C(=O)C(CCN1CCC(O)(CC1)c1ccc(Cl)cc1)(c1ccc...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>305</th>\n",
       "      <td>BRD-K70358946-001-17-3</td>\n",
       "      <td>CEUORZQYGODEFX-UHFFFAOYSA-N</td>\n",
       "      <td>aripiprazole</td>\n",
       "      <td>60795.0</td>\n",
       "      <td>HTR3A</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Clc1cccc(N2CCN(CCCCOc3ccc4CCC(=O)Nc4c3)CC2)c1Cl</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>306</th>\n",
       "      <td>NaN</td>\n",
       "      <td>IAZDPXIOMUYVGZ-UHFFFAOYSA-N</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>679.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>control</td>\n",
       "      <td>negcon</td>\n",
       "      <td>CS(=O)C</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>307 rows × 8 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "               broad_sample                     InChIKey  \\\n",
       "0    BRD-A86665761-001-01-1  TZDUHAJSIBHXDL-UHFFFAOYSA-N   \n",
       "1    BRD-A22032524-074-09-9  HTIQEAQVCYTUBX-UHFFFAOYSA-N   \n",
       "2    BRD-A01078468-001-14-8  PBBGSZCBWVPOOL-UHFFFAOYSA-N   \n",
       "3    BRD-K48278478-001-01-2  LOUPRKONTZGTKE-AFHBHXEDSA-N   \n",
       "4    BRD-K36574127-001-01-3  NYNZQNWKBKUAII-KBXCAEBGSA-N   \n",
       "..                      ...                          ...   \n",
       "302  BRD-K24616672-003-20-1  MFDFERRIHVXMIY-UHFFFAOYSA-N   \n",
       "303  BRD-A82396632-008-30-8  BYBLEWFAAKGYCD-UHFFFAOYSA-N   \n",
       "304  BRD-K61250553-003-30-6  RDOIQAHITMMDAJ-UHFFFAOYSA-N   \n",
       "305  BRD-K70358946-001-17-3  CEUORZQYGODEFX-UHFFFAOYSA-N   \n",
       "306                     NaN  IAZDPXIOMUYVGZ-UHFFFAOYSA-N   \n",
       "\n",
       "               pert_iname  pubchem_cid      gene pert_type control_type  \\\n",
       "0    gabapentin-enacarbil    9883933.0    CACNB4       trt          NaN   \n",
       "1              amlodipine       2162.0  CACNA2D3       trt          NaN   \n",
       "2               hexestrol       3606.0    AKR1C1       trt          NaN   \n",
       "3                 quinine      94175.0     KCNN4       trt          NaN   \n",
       "4                LOXO-101   46188928.0     NTRK1       trt          NaN   \n",
       "..                    ...          ...       ...       ...          ...   \n",
       "302              procaine       4914.0     HTR3A       trt          NaN   \n",
       "303            miconazole       4189.0     KCNN1       trt          NaN   \n",
       "304            loperamide       3955.0     OPRM1       trt          NaN   \n",
       "305          aripiprazole      60795.0     HTR3A       trt          NaN   \n",
       "306                  DMSO        679.0       NaN   control       negcon   \n",
       "\n",
       "                                                smiles  \n",
       "0             CC(C)C(=O)OC(C)OC(=O)NCC1(CC(O)=O)CCCCC1  \n",
       "1      CCOC(=O)C1=C(COCCN)NC(C)=C(C1c1ccccc1Cl)C(=O)OC  \n",
       "2                     CCC(C(CC)c1ccc(O)cc1)c1ccc(O)cc1  \n",
       "3    COc1ccc2nccc([C@@H](O)[C@H]3C[C@@H]4CC[N@]3C[C...  \n",
       "4    O[C@H]1CCN(C1)C(=O)Nc1cnn2ccc(nc12)N1CCC[C@@H]...  \n",
       "..                                                 ...  \n",
       "302                         CCN(CC)CCOC(=O)c1ccc(N)cc1  \n",
       "303        Clc1ccc(COC(Cn2ccnc2)c2ccc(Cl)cc2Cl)c(Cl)c1  \n",
       "304  CN(C)C(=O)C(CCN1CCC(O)(CC1)c1ccc(Cl)cc1)(c1ccc...  \n",
       "305    Clc1cccc(N2CCN(CCCCOc3ccc4CCC(=O)Nc4c3)CC2)c1Cl  \n",
       "306                                            CS(=O)C  \n",
       "\n",
       "[307 rows x 8 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "jump_metadata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "metadata": {},
   "outputs": [],
   "source": [
    "drug = \"Olanzapine\"\n",
    "inchikey = drug_metadata[drug_metadata.drug.isin([drug])][\"InChIKey\"].values[0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array(['HTR2C', 'HTR3A', 'ADRA2B', 'GABRB2', 'CHRM3', 'CHRM2', 'HRH4'],\n",
       "      dtype=object)"
      ]
     },
     "execution_count": 48,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sim_df[sim_df.InChIKey.isin([inchikey])][\"Metadata_matching_target\"].unique() #.sort_values(by=\"cosine_similarity\", ascending=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Cell</th>\n",
       "      <th>Genetic_Perturbation</th>\n",
       "      <th>Modality_1_timepoint</th>\n",
       "      <th>Modality_2_timepoint</th>\n",
       "      <th>cosine_sim</th>\n",
       "      <th>broad_sample</th>\n",
       "      <th>Metadata_matching_target</th>\n",
       "      <th>InChIKey</th>\n",
       "      <th>smiles</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>A549</td>\n",
       "      <td>CRISPR</td>\n",
       "      <td>long</td>\n",
       "      <td>long</td>\n",
       "      <td>-0.588253</td>\n",
       "      <td>BRD-A89164055-001-03-3</td>\n",
       "      <td>AKR1B1</td>\n",
       "      <td>LXANPKRCLVQAOG-UHFFFAOYSA-N</td>\n",
       "      <td>Fc1ccc2OCCC3(NC(=O)NC3=O)c2c1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>A549</td>\n",
       "      <td>CRISPR</td>\n",
       "      <td>long</td>\n",
       "      <td>long</td>\n",
       "      <td>-0.576196</td>\n",
       "      <td>BRD-A74391928-051-03-9</td>\n",
       "      <td>CACNG1</td>\n",
       "      <td>ALOBUEHUHMBRLE-UHFFFAOYSA-N</td>\n",
       "      <td>CCCCCCCN(CC)CCCC(O)c1ccc(NS(C)(=O)=O)cc1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>A549</td>\n",
       "      <td>CRISPR</td>\n",
       "      <td>long</td>\n",
       "      <td>long</td>\n",
       "      <td>-0.549354</td>\n",
       "      <td>BRD-K08893438-001-06-4</td>\n",
       "      <td>RGS4</td>\n",
       "      <td>QUIIIYITNGOFEI-UHFFFAOYSA-N</td>\n",
       "      <td>Cc1ccc(cc1)-n1sc(=O)n(Cc2ccc(F)cc2)c1=O</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>A549</td>\n",
       "      <td>CRISPR</td>\n",
       "      <td>long</td>\n",
       "      <td>long</td>\n",
       "      <td>-0.501251</td>\n",
       "      <td>BRD-K38512030-001-01-7</td>\n",
       "      <td>SLCO2B1</td>\n",
       "      <td>HJYYPODYNSCCOU-ODRIEIDWSA-N</td>\n",
       "      <td>CO[C@H]1\\C=C\\O[C@@]2(C)Oc3c(C2=O)c2c(O)cc(NC(=...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>A549</td>\n",
       "      <td>CRISPR</td>\n",
       "      <td>long</td>\n",
       "      <td>long</td>\n",
       "      <td>-0.433312</td>\n",
       "      <td>BRD-K22482860-001-20-6</td>\n",
       "      <td>KCNH7</td>\n",
       "      <td>NUKYPUAOHBNCPY-UHFFFAOYSA-N</td>\n",
       "      <td>Nc1ccncc1</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>7451</th>\n",
       "      <td>U2OS</td>\n",
       "      <td>ORF</td>\n",
       "      <td>short</td>\n",
       "      <td>short</td>\n",
       "      <td>0.616746</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>BRD4</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7452</th>\n",
       "      <td>U2OS</td>\n",
       "      <td>ORF</td>\n",
       "      <td>short</td>\n",
       "      <td>short</td>\n",
       "      <td>0.644838</td>\n",
       "      <td>BRD-K93779381-001-01-9</td>\n",
       "      <td>PRKCE</td>\n",
       "      <td>VDJHFHXMUKFKET-WDUFCVPESA-N</td>\n",
       "      <td>C\\C=C(\\C)C(=O)O[C@H]1C(C)=C[C@@]23[C@H](C)C[C@...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7453</th>\n",
       "      <td>U2OS</td>\n",
       "      <td>ORF</td>\n",
       "      <td>short</td>\n",
       "      <td>short</td>\n",
       "      <td>0.701634</td>\n",
       "      <td>BRD-K44227013-001-08-0</td>\n",
       "      <td>LYN</td>\n",
       "      <td>PHXJVRSECIGDHY-UHFFFAOYSA-N</td>\n",
       "      <td>CN1CCN(Cc2ccc(NC(=O)c3ccc(C)c(c3)C#Cc3cnc4cccn...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7454</th>\n",
       "      <td>U2OS</td>\n",
       "      <td>ORF</td>\n",
       "      <td>short</td>\n",
       "      <td>short</td>\n",
       "      <td>0.702138</td>\n",
       "      <td>BRD-K95785537-001-22-3</td>\n",
       "      <td>ABL1</td>\n",
       "      <td>PBBRWFOVCUAONR-UHFFFAOYSA-N</td>\n",
       "      <td>CC(C)(C)n1nc(-c2ccc(Cl)cc2)c2c(N)ncnc12</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7455</th>\n",
       "      <td>U2OS</td>\n",
       "      <td>ORF</td>\n",
       "      <td>short</td>\n",
       "      <td>short</td>\n",
       "      <td>0.714925</td>\n",
       "      <td>BRD-K77060810-001-01-5</td>\n",
       "      <td>P2RY12</td>\n",
       "      <td>NEMHKCNXXRQYRF-UHFFFAOYSA-N</td>\n",
       "      <td>CCOC(=O)c1cc(C#N)c(nc1C)N1CCC(CC1)C(=O)NS(=O)(...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>7456 rows × 9 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      Cell Genetic_Perturbation Modality_1_timepoint Modality_2_timepoint  \\\n",
       "0     A549               CRISPR                 long                 long   \n",
       "1     A549               CRISPR                 long                 long   \n",
       "2     A549               CRISPR                 long                 long   \n",
       "3     A549               CRISPR                 long                 long   \n",
       "4     A549               CRISPR                 long                 long   \n",
       "...    ...                  ...                  ...                  ...   \n",
       "7451  U2OS                  ORF                short                short   \n",
       "7452  U2OS                  ORF                short                short   \n",
       "7453  U2OS                  ORF                short                short   \n",
       "7454  U2OS                  ORF                short                short   \n",
       "7455  U2OS                  ORF                short                short   \n",
       "\n",
       "      cosine_sim            broad_sample Metadata_matching_target  \\\n",
       "0      -0.588253  BRD-A89164055-001-03-3                   AKR1B1   \n",
       "1      -0.576196  BRD-A74391928-051-03-9                   CACNG1   \n",
       "2      -0.549354  BRD-K08893438-001-06-4                     RGS4   \n",
       "3      -0.501251  BRD-K38512030-001-01-7                  SLCO2B1   \n",
       "4      -0.433312  BRD-K22482860-001-20-6                    KCNH7   \n",
       "...          ...                     ...                      ...   \n",
       "7451    0.616746  BRD-K64890080-001-02-1                     BRD4   \n",
       "7452    0.644838  BRD-K93779381-001-01-9                    PRKCE   \n",
       "7453    0.701634  BRD-K44227013-001-08-0                      LYN   \n",
       "7454    0.702138  BRD-K95785537-001-22-3                     ABL1   \n",
       "7455    0.714925  BRD-K77060810-001-01-5                   P2RY12   \n",
       "\n",
       "                         InChIKey  \\\n",
       "0     LXANPKRCLVQAOG-UHFFFAOYSA-N   \n",
       "1     ALOBUEHUHMBRLE-UHFFFAOYSA-N   \n",
       "2     QUIIIYITNGOFEI-UHFFFAOYSA-N   \n",
       "3     HJYYPODYNSCCOU-ODRIEIDWSA-N   \n",
       "4     NUKYPUAOHBNCPY-UHFFFAOYSA-N   \n",
       "...                           ...   \n",
       "7451  XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "7452  VDJHFHXMUKFKET-WDUFCVPESA-N   \n",
       "7453  PHXJVRSECIGDHY-UHFFFAOYSA-N   \n",
       "7454  PBBRWFOVCUAONR-UHFFFAOYSA-N   \n",
       "7455  NEMHKCNXXRQYRF-UHFFFAOYSA-N   \n",
       "\n",
       "                                                 smiles  \n",
       "0                         Fc1ccc2OCCC3(NC(=O)NC3=O)c2c1  \n",
       "1              CCCCCCCN(CC)CCCC(O)c1ccc(NS(C)(=O)=O)cc1  \n",
       "2               Cc1ccc(cc1)-n1sc(=O)n(Cc2ccc(F)cc2)c1=O  \n",
       "3     CO[C@H]1\\C=C\\O[C@@]2(C)Oc3c(C2=O)c2c(O)cc(NC(=...  \n",
       "4                                             Nc1ccncc1  \n",
       "...                                                 ...  \n",
       "7451  CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "7452  C\\C=C(\\C)C(=O)O[C@H]1C(C)=C[C@@]23[C@H](C)C[C@...  \n",
       "7453  CN1CCN(Cc2ccc(NC(=O)c3ccc(C)c(c3)C#Cc3cnc4cccn...  \n",
       "7454            CC(C)(C)n1nc(-c2ccc(Cl)cc2)c2c(N)ncnc12  \n",
       "7455  CCOC(=O)c1cc(C#N)c(nc1C)N1CCC(CC1)C(=O)NS(=O)(...  \n",
       "\n",
       "[7456 rows x 9 columns]"
      ]
     },
     "execution_count": 52,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sim_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [],
   "source": [
    "jump_path = pathlib.Path(\"/home/ubuntu/giovanni\")\n",
    "tahoe_data = pd.read_csv(jump_path/\"data/drug_metadata_inchikey.csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [],
   "source": [
    "jump_metadata = pd.read_csv(path/\"code/2024_Chandrasekaran_NatureMethods/metadata/external_metadata/JUMP-Target-1_compound_metadata_targets.tsv\", sep=\"\\t\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['Salicylic acid',\n",
       " '5-Azacytidine',\n",
       " 'Larotrectinib',\n",
       " 'Filgotinib',\n",
       " 'Cilostazol',\n",
       " 'Lonafarnib',\n",
       " 'Acetohexamide',\n",
       " 'Homoharringtonine',\n",
       " 'Ponatinib',\n",
       " 'Nevirapine',\n",
       " 'Menadione',\n",
       " 'Olanzapine',\n",
       " 'Dexamethasone',\n",
       " 'Cyclosporin A',\n",
       " 'Regorafenib',\n",
       " 'Tranilast',\n",
       " 'Quinidine (15% dihydroquinidine)']"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tahoe_data[[\"InChIKey\", \"drug\"]].dropna()[\"drug\"].tolist()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [],
   "source": [
    "tahoe_data = pd.merge(tahoe_data, jump_metadata[[\"InChIKey\", \"target_list\"]], on='InChIKey',\n",
    "    how='left')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'AKR1C1|PTGS1|PTGS2'"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pd.read_csv(path/'data/drug_metadata_inchikey.csv')['target_list'].dropna().unique()[0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['AOX1',\n",
       " 'BGLAP',\n",
       " 'F10',\n",
       " 'F2',\n",
       " 'F7',\n",
       " 'F9',\n",
       " 'GGCX',\n",
       " 'NQO1',\n",
       " 'NQO2',\n",
       " 'PROC',\n",
       " 'PROS1',\n",
       " 'PROZ',\n",
       " 'VKORC1',\n",
       " 'VKORC1L1']"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "print(f\"The known targets from the JUMP dataset are: {', '.join(pd.read_csv(path/'data/drug_metadata_inchikey.csv')['target_list'].dropna().unique()[10].split('|'))}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ORF: 6 positive correlations (>0.2), 3 negative correlations (<-0.2)\n",
      "CRISPR: 14 positive correlations (>0.2), 0 negative correlations (<-0.2)\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        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>Cell</th>\n",
       "      <th>Genetic_Perturbation</th>\n",
       "      <th>Modality_1_timepoint</th>\n",
       "      <th>Modality_2_timepoint</th>\n",
       "      <th>cosine_sim</th>\n",
       "      <th>broad_sample</th>\n",
       "      <th>Metadata_matching_target</th>\n",
       "      <th>InChIKey</th>\n",
       "      <th>smiles</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>449</th>\n",
       "      <td>A549</td>\n",
       "      <td>CRISPR</td>\n",
       "      <td>long</td>\n",
       "      <td>long</td>\n",
       "      <td>0.550335</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>BRD4</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>463</th>\n",
       "      <td>A549</td>\n",
       "      <td>CRISPR</td>\n",
       "      <td>long</td>\n",
       "      <td>long</td>\n",
       "      <td>0.748997</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>PLK1</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>902</th>\n",
       "      <td>A549</td>\n",
       "      <td>CRISPR</td>\n",
       "      <td>long</td>\n",
       "      <td>short</td>\n",
       "      <td>0.536371</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>BRD4</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>930</th>\n",
       "      <td>A549</td>\n",
       "      <td>CRISPR</td>\n",
       "      <td>long</td>\n",
       "      <td>short</td>\n",
       "      <td>0.773190</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>PLK1</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1256</th>\n",
       "      <td>A549</td>\n",
       "      <td>CRISPR</td>\n",
       "      <td>short</td>\n",
       "      <td>long</td>\n",
       "      <td>0.218241</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>BRD4</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1397</th>\n",
       "      <td>A549</td>\n",
       "      <td>CRISPR</td>\n",
       "      <td>short</td>\n",
       "      <td>long</td>\n",
       "      <td>0.762776</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>PLK1</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1708</th>\n",
       "      <td>A549</td>\n",
       "      <td>CRISPR</td>\n",
       "      <td>short</td>\n",
       "      <td>short</td>\n",
       "      <td>0.217543</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>BRD4</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1863</th>\n",
       "      <td>A549</td>\n",
       "      <td>CRISPR</td>\n",
       "      <td>short</td>\n",
       "      <td>short</td>\n",
       "      <td>0.746296</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>PLK1</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1918</th>\n",
       "      <td>A549</td>\n",
       "      <td>ORF</td>\n",
       "      <td>long</td>\n",
       "      <td>long</td>\n",
       "      <td>-0.218416</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>BRD4</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2262</th>\n",
       "      <td>A549</td>\n",
       "      <td>ORF</td>\n",
       "      <td>long</td>\n",
       "      <td>long</td>\n",
       "      <td>0.316084</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>PLK1</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2352</th>\n",
       "      <td>A549</td>\n",
       "      <td>ORF</td>\n",
       "      <td>long</td>\n",
       "      <td>short</td>\n",
       "      <td>-0.329261</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>BRD4</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2459</th>\n",
       "      <td>A549</td>\n",
       "      <td>ORF</td>\n",
       "      <td>long</td>\n",
       "      <td>short</td>\n",
       "      <td>-0.079798</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>PLK1</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2893</th>\n",
       "      <td>A549</td>\n",
       "      <td>ORF</td>\n",
       "      <td>short</td>\n",
       "      <td>long</td>\n",
       "      <td>-0.105228</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>BRD4</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3165</th>\n",
       "      <td>A549</td>\n",
       "      <td>ORF</td>\n",
       "      <td>short</td>\n",
       "      <td>long</td>\n",
       "      <td>0.293320</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>PLK1</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3316</th>\n",
       "      <td>A549</td>\n",
       "      <td>ORF</td>\n",
       "      <td>short</td>\n",
       "      <td>short</td>\n",
       "      <td>-0.247933</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>BRD4</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3396</th>\n",
       "      <td>A549</td>\n",
       "      <td>ORF</td>\n",
       "      <td>short</td>\n",
       "      <td>short</td>\n",
       "      <td>-0.105536</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>PLK1</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4095</th>\n",
       "      <td>U2OS</td>\n",
       "      <td>CRISPR</td>\n",
       "      <td>long</td>\n",
       "      <td>long</td>\n",
       "      <td>0.267729</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>BRD4</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4193</th>\n",
       "      <td>U2OS</td>\n",
       "      <td>CRISPR</td>\n",
       "      <td>long</td>\n",
       "      <td>long</td>\n",
       "      <td>0.683034</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>PLK1</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4325</th>\n",
       "      <td>U2OS</td>\n",
       "      <td>CRISPR</td>\n",
       "      <td>long</td>\n",
       "      <td>short</td>\n",
       "      <td>-0.016004</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>BRD4</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4659</th>\n",
       "      <td>U2OS</td>\n",
       "      <td>CRISPR</td>\n",
       "      <td>long</td>\n",
       "      <td>short</td>\n",
       "      <td>0.891863</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>PLK1</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4994</th>\n",
       "      <td>U2OS</td>\n",
       "      <td>CRISPR</td>\n",
       "      <td>short</td>\n",
       "      <td>long</td>\n",
       "      <td>0.229830</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>BRD4</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5124</th>\n",
       "      <td>U2OS</td>\n",
       "      <td>CRISPR</td>\n",
       "      <td>short</td>\n",
       "      <td>long</td>\n",
       "      <td>0.650440</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>PLK1</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5283</th>\n",
       "      <td>U2OS</td>\n",
       "      <td>CRISPR</td>\n",
       "      <td>short</td>\n",
       "      <td>short</td>\n",
       "      <td>-0.007166</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>BRD4</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5591</th>\n",
       "      <td>U2OS</td>\n",
       "      <td>CRISPR</td>\n",
       "      <td>short</td>\n",
       "      <td>short</td>\n",
       "      <td>0.893123</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>PLK1</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5805</th>\n",
       "      <td>U2OS</td>\n",
       "      <td>ORF</td>\n",
       "      <td>long</td>\n",
       "      <td>long</td>\n",
       "      <td>0.045007</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>PLK1</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6057</th>\n",
       "      <td>U2OS</td>\n",
       "      <td>ORF</td>\n",
       "      <td>long</td>\n",
       "      <td>long</td>\n",
       "      <td>0.608289</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>BRD4</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6117</th>\n",
       "      <td>U2OS</td>\n",
       "      <td>ORF</td>\n",
       "      <td>long</td>\n",
       "      <td>short</td>\n",
       "      <td>-0.187308</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>PLK1</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6515</th>\n",
       "      <td>U2OS</td>\n",
       "      <td>ORF</td>\n",
       "      <td>long</td>\n",
       "      <td>short</td>\n",
       "      <td>0.574759</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>BRD4</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6802</th>\n",
       "      <td>U2OS</td>\n",
       "      <td>ORF</td>\n",
       "      <td>short</td>\n",
       "      <td>long</td>\n",
       "      <td>0.113212</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>PLK1</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6984</th>\n",
       "      <td>U2OS</td>\n",
       "      <td>ORF</td>\n",
       "      <td>short</td>\n",
       "      <td>long</td>\n",
       "      <td>0.592689</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>BRD4</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7093</th>\n",
       "      <td>U2OS</td>\n",
       "      <td>ORF</td>\n",
       "      <td>short</td>\n",
       "      <td>short</td>\n",
       "      <td>-0.097227</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>PLK1</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7451</th>\n",
       "      <td>U2OS</td>\n",
       "      <td>ORF</td>\n",
       "      <td>short</td>\n",
       "      <td>short</td>\n",
       "      <td>0.616746</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>BRD4</td>\n",
       "      <td>XQVVPGYIWAGRNI-JOCHJYFZSA-N</td>\n",
       "      <td>CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      Cell Genetic_Perturbation Modality_1_timepoint Modality_2_timepoint  \\\n",
       "449   A549               CRISPR                 long                 long   \n",
       "463   A549               CRISPR                 long                 long   \n",
       "902   A549               CRISPR                 long                short   \n",
       "930   A549               CRISPR                 long                short   \n",
       "1256  A549               CRISPR                short                 long   \n",
       "1397  A549               CRISPR                short                 long   \n",
       "1708  A549               CRISPR                short                short   \n",
       "1863  A549               CRISPR                short                short   \n",
       "1918  A549                  ORF                 long                 long   \n",
       "2262  A549                  ORF                 long                 long   \n",
       "2352  A549                  ORF                 long                short   \n",
       "2459  A549                  ORF                 long                short   \n",
       "2893  A549                  ORF                short                 long   \n",
       "3165  A549                  ORF                short                 long   \n",
       "3316  A549                  ORF                short                short   \n",
       "3396  A549                  ORF                short                short   \n",
       "4095  U2OS               CRISPR                 long                 long   \n",
       "4193  U2OS               CRISPR                 long                 long   \n",
       "4325  U2OS               CRISPR                 long                short   \n",
       "4659  U2OS               CRISPR                 long                short   \n",
       "4994  U2OS               CRISPR                short                 long   \n",
       "5124  U2OS               CRISPR                short                 long   \n",
       "5283  U2OS               CRISPR                short                short   \n",
       "5591  U2OS               CRISPR                short                short   \n",
       "5805  U2OS                  ORF                 long                 long   \n",
       "6057  U2OS                  ORF                 long                 long   \n",
       "6117  U2OS                  ORF                 long                short   \n",
       "6515  U2OS                  ORF                 long                short   \n",
       "6802  U2OS                  ORF                short                 long   \n",
       "6984  U2OS                  ORF                short                 long   \n",
       "7093  U2OS                  ORF                short                short   \n",
       "7451  U2OS                  ORF                short                short   \n",
       "\n",
       "      cosine_sim            broad_sample Metadata_matching_target  \\\n",
       "449     0.550335  BRD-K64890080-001-02-1                     BRD4   \n",
       "463     0.748997  BRD-K64890080-001-02-1                     PLK1   \n",
       "902     0.536371  BRD-K64890080-001-02-1                     BRD4   \n",
       "930     0.773190  BRD-K64890080-001-02-1                     PLK1   \n",
       "1256    0.218241  BRD-K64890080-001-02-1                     BRD4   \n",
       "1397    0.762776  BRD-K64890080-001-02-1                     PLK1   \n",
       "1708    0.217543  BRD-K64890080-001-02-1                     BRD4   \n",
       "1863    0.746296  BRD-K64890080-001-02-1                     PLK1   \n",
       "1918   -0.218416  BRD-K64890080-001-02-1                     BRD4   \n",
       "2262    0.316084  BRD-K64890080-001-02-1                     PLK1   \n",
       "2352   -0.329261  BRD-K64890080-001-02-1                     BRD4   \n",
       "2459   -0.079798  BRD-K64890080-001-02-1                     PLK1   \n",
       "2893   -0.105228  BRD-K64890080-001-02-1                     BRD4   \n",
       "3165    0.293320  BRD-K64890080-001-02-1                     PLK1   \n",
       "3316   -0.247933  BRD-K64890080-001-02-1                     BRD4   \n",
       "3396   -0.105536  BRD-K64890080-001-02-1                     PLK1   \n",
       "4095    0.267729  BRD-K64890080-001-02-1                     BRD4   \n",
       "4193    0.683034  BRD-K64890080-001-02-1                     PLK1   \n",
       "4325   -0.016004  BRD-K64890080-001-02-1                     BRD4   \n",
       "4659    0.891863  BRD-K64890080-001-02-1                     PLK1   \n",
       "4994    0.229830  BRD-K64890080-001-02-1                     BRD4   \n",
       "5124    0.650440  BRD-K64890080-001-02-1                     PLK1   \n",
       "5283   -0.007166  BRD-K64890080-001-02-1                     BRD4   \n",
       "5591    0.893123  BRD-K64890080-001-02-1                     PLK1   \n",
       "5805    0.045007  BRD-K64890080-001-02-1                     PLK1   \n",
       "6057    0.608289  BRD-K64890080-001-02-1                     BRD4   \n",
       "6117   -0.187308  BRD-K64890080-001-02-1                     PLK1   \n",
       "6515    0.574759  BRD-K64890080-001-02-1                     BRD4   \n",
       "6802    0.113212  BRD-K64890080-001-02-1                     PLK1   \n",
       "6984    0.592689  BRD-K64890080-001-02-1                     BRD4   \n",
       "7093   -0.097227  BRD-K64890080-001-02-1                     PLK1   \n",
       "7451    0.616746  BRD-K64890080-001-02-1                     BRD4   \n",
       "\n",
       "                         InChIKey  \\\n",
       "449   XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "463   XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "902   XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "930   XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "1256  XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "1397  XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "1708  XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "1863  XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "1918  XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "2262  XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "2352  XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "2459  XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "2893  XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "3165  XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "3316  XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "3396  XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "4095  XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "4193  XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "4325  XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "4659  XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "4994  XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "5124  XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "5283  XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "5591  XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "5805  XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "6057  XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "6117  XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "6515  XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "6802  XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "6984  XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "7093  XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "7451  XQVVPGYIWAGRNI-JOCHJYFZSA-N   \n",
       "\n",
       "                                                 smiles  \n",
       "449   CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "463   CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "902   CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "930   CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "1256  CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "1397  CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "1708  CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "1863  CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "1918  CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "2262  CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "2352  CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "2459  CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "2893  CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "3165  CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "3316  CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "3396  CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "4095  CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "4193  CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "4325  CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "4659  CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "4994  CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "5124  CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "5283  CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "5591  CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "5805  CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "6057  CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "6117  CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "6515  CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "6802  CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "6984  CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "7093  CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  \n",
       "7451  CC[C@H]1N(C2CCCC2)c2nc(Nc3ccc(cc3OC)C(=O)NC3CC...  "
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cosine_similarity = pd.read_csv(path/ \"data/compound_genetic_perturbation_cosine_similarity_inchikey.csv\")\n",
    "inchikey = \"XQVVPGYIWAGRNI-JOCHJYFZSA-N\"\n",
    "# Filter for the specific InChIKey\n",
    "filtered_df = cosine_similarity[cosine_similarity.InChIKey.isin([inchikey])]\n",
    "\n",
    "# Count ORF entries with cosine_similarity > 0.2 and < -0.2\n",
    "orf_positive = filtered_df[(filtered_df.Genetic_Perturbation == 'ORF') & (filtered_df.cosine_sim > 0.2)].shape[0]\n",
    "orf_negative = filtered_df[(filtered_df.Genetic_Perturbation == 'ORF') & (filtered_df.cosine_sim < -0.2)].shape[0]\n",
    "\n",
    "# Count CRISPR entries with cosine_similarity > 0.2 and < -0.2\n",
    "crispr_positive = filtered_df[(filtered_df.Genetic_Perturbation == 'CRISPR') & (filtered_df.cosine_sim > 0.2)].shape[0]\n",
    "crispr_negative = filtered_df[(filtered_df.Genetic_Perturbation == 'CRISPR') & (filtered_df.cosine_sim < -0.2)].shape[0]\n",
    "\n",
    "print(f\"ORF: {orf_positive} positive correlations (>0.2), {orf_negative} negative correlations (<-0.2)\")\n",
    "print(f\"CRISPR: {crispr_positive} positive correlations (>0.2), {crispr_negative} negative correlations (<-0.2)\")\n",
    "\n",
    "# Return the filtered dataframe\n",
    "filtered_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Cell</th>\n",
       "      <th>Genetic_Perturbation</th>\n",
       "      <th>Modality_1_timepoint</th>\n",
       "      <th>Modality_2_timepoint</th>\n",
       "      <th>cosine_sim</th>\n",
       "      <th>Metadata_broad_sample</th>\n",
       "      <th>Metadata_matching_target</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>A549</td>\n",
       "      <td>CRISPR</td>\n",
       "      <td>long</td>\n",
       "      <td>long</td>\n",
       "      <td>-0.588253</td>\n",
       "      <td>BRD-A89164055-001-03-3</td>\n",
       "      <td>AKR1B1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>A549</td>\n",
       "      <td>CRISPR</td>\n",
       "      <td>long</td>\n",
       "      <td>long</td>\n",
       "      <td>-0.576196</td>\n",
       "      <td>BRD-A74391928-051-03-9</td>\n",
       "      <td>CACNG1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>A549</td>\n",
       "      <td>CRISPR</td>\n",
       "      <td>long</td>\n",
       "      <td>long</td>\n",
       "      <td>-0.549354</td>\n",
       "      <td>BRD-K08893438-001-06-4</td>\n",
       "      <td>RGS4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>A549</td>\n",
       "      <td>CRISPR</td>\n",
       "      <td>long</td>\n",
       "      <td>long</td>\n",
       "      <td>-0.501251</td>\n",
       "      <td>BRD-K38512030-001-01-7</td>\n",
       "      <td>SLCO2B1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>A549</td>\n",
       "      <td>CRISPR</td>\n",
       "      <td>long</td>\n",
       "      <td>long</td>\n",
       "      <td>-0.433312</td>\n",
       "      <td>BRD-K22482860-001-20-6</td>\n",
       "      <td>KCNH7</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7451</th>\n",
       "      <td>U2OS</td>\n",
       "      <td>ORF</td>\n",
       "      <td>short</td>\n",
       "      <td>short</td>\n",
       "      <td>0.616746</td>\n",
       "      <td>BRD-K64890080-001-02-1</td>\n",
       "      <td>BRD4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7452</th>\n",
       "      <td>U2OS</td>\n",
       "      <td>ORF</td>\n",
       "      <td>short</td>\n",
       "      <td>short</td>\n",
       "      <td>0.644838</td>\n",
       "      <td>BRD-K93779381-001-01-9</td>\n",
       "      <td>PRKCE</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7453</th>\n",
       "      <td>U2OS</td>\n",
       "      <td>ORF</td>\n",
       "      <td>short</td>\n",
       "      <td>short</td>\n",
       "      <td>0.701634</td>\n",
       "      <td>BRD-K44227013-001-08-0</td>\n",
       "      <td>LYN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7454</th>\n",
       "      <td>U2OS</td>\n",
       "      <td>ORF</td>\n",
       "      <td>short</td>\n",
       "      <td>short</td>\n",
       "      <td>0.702138</td>\n",
       "      <td>BRD-K95785537-001-22-3</td>\n",
       "      <td>ABL1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7455</th>\n",
       "      <td>U2OS</td>\n",
       "      <td>ORF</td>\n",
       "      <td>short</td>\n",
       "      <td>short</td>\n",
       "      <td>0.714925</td>\n",
       "      <td>BRD-K77060810-001-01-5</td>\n",
       "      <td>P2RY12</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>7456 rows × 7 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      Cell Genetic_Perturbation Modality_1_timepoint Modality_2_timepoint  \\\n",
       "0     A549               CRISPR                 long                 long   \n",
       "1     A549               CRISPR                 long                 long   \n",
       "2     A549               CRISPR                 long                 long   \n",
       "3     A549               CRISPR                 long                 long   \n",
       "4     A549               CRISPR                 long                 long   \n",
       "...    ...                  ...                  ...                  ...   \n",
       "7451  U2OS                  ORF                short                short   \n",
       "7452  U2OS                  ORF                short                short   \n",
       "7453  U2OS                  ORF                short                short   \n",
       "7454  U2OS                  ORF                short                short   \n",
       "7455  U2OS                  ORF                short                short   \n",
       "\n",
       "      cosine_sim   Metadata_broad_sample Metadata_matching_target  \n",
       "0      -0.588253  BRD-A89164055-001-03-3                   AKR1B1  \n",
       "1      -0.576196  BRD-A74391928-051-03-9                   CACNG1  \n",
       "2      -0.549354  BRD-K08893438-001-06-4                     RGS4  \n",
       "3      -0.501251  BRD-K38512030-001-01-7                  SLCO2B1  \n",
       "4      -0.433312  BRD-K22482860-001-20-6                    KCNH7  \n",
       "...          ...                     ...                      ...  \n",
       "7451    0.616746  BRD-K64890080-001-02-1                     BRD4  \n",
       "7452    0.644838  BRD-K93779381-001-01-9                    PRKCE  \n",
       "7453    0.701634  BRD-K44227013-001-08-0                      LYN  \n",
       "7454    0.702138  BRD-K95785537-001-22-3                     ABL1  \n",
       "7455    0.714925  BRD-K77060810-001-01-5                   P2RY12  \n",
       "\n",
       "[7456 rows x 7 columns]"
      ]
     },
     "execution_count": 51,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pd.read_csv(jump_path/\"code/2024_Chandrasekaran_NatureMethods/benchmark/output/compound_genetic_perturbation_cosine_similarity.csv\")"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.11.12"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}