exploration.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "path = 'path-to-data-repository'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>doi</th>\n",
       "      <th>bioActivity</th>\n",
       "      <th>collectionSpecie</th>\n",
       "      <th>collectionSite</th>\n",
       "      <th>collectionType</th>\n",
       "      <th>molType</th>\n",
       "      <th>molecularMass</th>\n",
       "      <th>monoisotropicMass</th>\n",
       "      <th>cLogP</th>\n",
       "      <th>tpsa</th>\n",
       "      <th>numberOfLipinskiViolations</th>\n",
       "      <th>numberOfH_bondAcceptors</th>\n",
       "      <th>numberOfH_bondDonors</th>\n",
       "      <th>numberOfRotableBonds</th>\n",
       "      <th>molecularVolume</th>\n",
       "      <th>smile</th>\n",
       "      <th>name</th>\n",
       "      <th>file_name</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>10.1016/j.biortech.2010.01.041</td>\n",
       "      <td>Inhibition of Protease</td>\n",
       "      <td>Piper crassinervium (Piperaceae)</td>\n",
       "      <td>Araraquara/SP</td>\n",
       "      <td>Biotransformation Product</td>\n",
       "      <td>http://nubbe.db/AromaticDerivative</td>\n",
       "      <td>290,354187</td>\n",
       "      <td>290,1517944</td>\n",
       "      <td>4,660999775</td>\n",
       "      <td>66,76100159</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>282,9689941</td>\n",
       "      <td>O=C(OC/C=C(C)/CC/C=C(C)/C)C1=CC(O)=C(O)C=C1</td>\n",
       "      <td>3,4-dihydroxybenzoic acid geranyl ester</td>\n",
       "      <td>10.1016@j.biortech.2010.01.041.pdf</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>10.1016/j.biortech.2010.01.041</td>\n",
       "      <td>Inhibition of Protease</td>\n",
       "      <td>Piper crassinervium (Piperaceae)</td>\n",
       "      <td>Araraquara/SP</td>\n",
       "      <td>Biotransformation Product</td>\n",
       "      <td>http://nubbe.db/ChemicalCompound</td>\n",
       "      <td>290,354187</td>\n",
       "      <td>290,1517944</td>\n",
       "      <td>4,660999775</td>\n",
       "      <td>66,76100159</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>282,9689941</td>\n",
       "      <td>O=C(OC/C=C(C)/CC/C=C(C)/C)C1=CC(O)=C(O)C=C1</td>\n",
       "      <td>3,4-dihydroxybenzoic acid geranyl ester</td>\n",
       "      <td>10.1016@j.biortech.2010.01.041.pdf</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>10.1016/j.biortech.2010.01.041</td>\n",
       "      <td>Inhibition of Protease</td>\n",
       "      <td>Piper crassinervium (Piperaceae)</td>\n",
       "      <td>Araraquara/SP</td>\n",
       "      <td>Biotransformation Product</td>\n",
       "      <td>http://nubbe.db/ChemicalSubstance</td>\n",
       "      <td>290,354187</td>\n",
       "      <td>290,1517944</td>\n",
       "      <td>4,660999775</td>\n",
       "      <td>66,76100159</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>282,9689941</td>\n",
       "      <td>O=C(OC/C=C(C)/CC/C=C(C)/C)C1=CC(O)=C(O)C=C1</td>\n",
       "      <td>3,4-dihydroxybenzoic acid geranyl ester</td>\n",
       "      <td>10.1016@j.biortech.2010.01.041.pdf</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>10.1016/j.biortech.2010.01.041</td>\n",
       "      <td>Antiviral</td>\n",
       "      <td>Piper crassinervium (Piperaceae)</td>\n",
       "      <td>Araraquara/SP</td>\n",
       "      <td>Biotransformation Product</td>\n",
       "      <td>http://nubbe.db/AromaticDerivative</td>\n",
       "      <td>290,354187</td>\n",
       "      <td>290,1517944</td>\n",
       "      <td>4,660999775</td>\n",
       "      <td>66,76100159</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>282,9689941</td>\n",
       "      <td>O=C(OC/C=C(C)/CC/C=C(C)/C)C1=CC(O)=C(O)C=C1</td>\n",
       "      <td>3,4-dihydroxybenzoic acid geranyl ester</td>\n",
       "      <td>10.1016@j.biortech.2010.01.041.pdf</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>10.1016/j.biortech.2010.01.041</td>\n",
       "      <td>Antiviral</td>\n",
       "      <td>Piper crassinervium (Piperaceae)</td>\n",
       "      <td>Araraquara/SP</td>\n",
       "      <td>Biotransformation Product</td>\n",
       "      <td>http://nubbe.db/ChemicalCompound</td>\n",
       "      <td>290,354187</td>\n",
       "      <td>290,1517944</td>\n",
       "      <td>4,660999775</td>\n",
       "      <td>66,76100159</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>282,9689941</td>\n",
       "      <td>O=C(OC/C=C(C)/CC/C=C(C)/C)C1=CC(O)=C(O)C=C1</td>\n",
       "      <td>3,4-dihydroxybenzoic acid geranyl ester</td>\n",
       "      <td>10.1016@j.biortech.2010.01.041.pdf</td>\n",
       "    </tr>\n",
       "    <tr>\n",
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       "    <tr>\n",
       "      <th>2299</th>\n",
       "      <td>10.1016/S0031-9422(00)94671-5</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
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       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>10.1016@S0031-9422(00)94671-5.pdf</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2300</th>\n",
       "      <td>10.1016/S0031-9422(00)80444-6</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
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       "      <td></td>\n",
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       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>10.1016@S0031-9422(00)80444-6.pdf</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2301</th>\n",
       "      <td>10.1021/np50032a021</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
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       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>10.1021@np50032a021.pdf</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2302</th>\n",
       "      <td>10.1016/S0031-9422(00)83467-6</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
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       "      <td></td>\n",
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       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>10.1016@S0031-9422(00)83467-6.pdf</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2303</th>\n",
       "      <td>10.1016/0031-9422(80)83208-0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>10.1016@0031-9422(80)83208-0.pdf</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2304 rows × 18 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                 doi             bioActivity  \\\n",
       "0     10.1016/j.biortech.2010.01.041  Inhibition of Protease   \n",
       "1     10.1016/j.biortech.2010.01.041  Inhibition of Protease   \n",
       "2     10.1016/j.biortech.2010.01.041  Inhibition of Protease   \n",
       "3     10.1016/j.biortech.2010.01.041               Antiviral   \n",
       "4     10.1016/j.biortech.2010.01.041               Antiviral   \n",
       "...                              ...                     ...   \n",
       "2299   10.1016/S0031-9422(00)94671-5                           \n",
       "2300   10.1016/S0031-9422(00)80444-6                           \n",
       "2301             10.1021/np50032a021                           \n",
       "2302   10.1016/S0031-9422(00)83467-6                           \n",
       "2303    10.1016/0031-9422(80)83208-0                           \n",
       "\n",
       "                      collectionSpecie collectionSite  \\\n",
       "0     Piper crassinervium (Piperaceae)  Araraquara/SP   \n",
       "1     Piper crassinervium (Piperaceae)  Araraquara/SP   \n",
       "2     Piper crassinervium (Piperaceae)  Araraquara/SP   \n",
       "3     Piper crassinervium (Piperaceae)  Araraquara/SP   \n",
       "4     Piper crassinervium (Piperaceae)  Araraquara/SP   \n",
       "...                                ...            ...   \n",
       "2299                                                    \n",
       "2300                                                    \n",
       "2301                                                    \n",
       "2302                                                    \n",
       "2303                                                    \n",
       "\n",
       "                 collectionType                             molType  \\\n",
       "0     Biotransformation Product  http://nubbe.db/AromaticDerivative   \n",
       "1     Biotransformation Product    http://nubbe.db/ChemicalCompound   \n",
       "2     Biotransformation Product   http://nubbe.db/ChemicalSubstance   \n",
       "3     Biotransformation Product  http://nubbe.db/AromaticDerivative   \n",
       "4     Biotransformation Product    http://nubbe.db/ChemicalCompound   \n",
       "...                         ...                                 ...   \n",
       "2299                                                                  \n",
       "2300                                                                  \n",
       "2301                                                                  \n",
       "2302                                                                  \n",
       "2303                                                                  \n",
       "\n",
       "     molecularMass monoisotropicMass        cLogP         tpsa  \\\n",
       "0       290,354187       290,1517944  4,660999775  66,76100159   \n",
       "1       290,354187       290,1517944  4,660999775  66,76100159   \n",
       "2       290,354187       290,1517944  4,660999775  66,76100159   \n",
       "3       290,354187       290,1517944  4,660999775  66,76100159   \n",
       "4       290,354187       290,1517944  4,660999775  66,76100159   \n",
       "...            ...               ...          ...          ...   \n",
       "2299                                                             \n",
       "2300                                                             \n",
       "2301                                                             \n",
       "2302                                                             \n",
       "2303                                                             \n",
       "\n",
       "     numberOfLipinskiViolations numberOfH_bondAcceptors numberOfH_bondDonors  \\\n",
       "0                           0.0                     4.0                  2.0   \n",
       "1                           0.0                     4.0                  2.0   \n",
       "2                           0.0                     4.0                  2.0   \n",
       "3                           0.0                     4.0                  2.0   \n",
       "4                           0.0                     4.0                  2.0   \n",
       "...                         ...                     ...                  ...   \n",
       "2299                                                                           \n",
       "2300                                                                           \n",
       "2301                                                                           \n",
       "2302                                                                           \n",
       "2303                                                                           \n",
       "\n",
       "     numberOfRotableBonds molecularVolume  \\\n",
       "0                     7.0     282,9689941   \n",
       "1                     7.0     282,9689941   \n",
       "2                     7.0     282,9689941   \n",
       "3                     7.0     282,9689941   \n",
       "4                     7.0     282,9689941   \n",
       "...                   ...             ...   \n",
       "2299                                        \n",
       "2300                                        \n",
       "2301                                        \n",
       "2302                                        \n",
       "2303                                        \n",
       "\n",
       "                                            smile  \\\n",
       "0     O=C(OC/C=C(C)/CC/C=C(C)/C)C1=CC(O)=C(O)C=C1   \n",
       "1     O=C(OC/C=C(C)/CC/C=C(C)/C)C1=CC(O)=C(O)C=C1   \n",
       "2     O=C(OC/C=C(C)/CC/C=C(C)/C)C1=CC(O)=C(O)C=C1   \n",
       "3     O=C(OC/C=C(C)/CC/C=C(C)/C)C1=CC(O)=C(O)C=C1   \n",
       "4     O=C(OC/C=C(C)/CC/C=C(C)/C)C1=CC(O)=C(O)C=C1   \n",
       "...                                           ...   \n",
       "2299                                                \n",
       "2300                                                \n",
       "2301                                                \n",
       "2302                                                \n",
       "2303                                                \n",
       "\n",
       "                                         name  \\\n",
       "0     3,4-dihydroxybenzoic acid geranyl ester   \n",
       "1     3,4-dihydroxybenzoic acid geranyl ester   \n",
       "2     3,4-dihydroxybenzoic acid geranyl ester   \n",
       "3     3,4-dihydroxybenzoic acid geranyl ester   \n",
       "4     3,4-dihydroxybenzoic acid geranyl ester   \n",
       "...                                       ...   \n",
       "2299                                            \n",
       "2300                                            \n",
       "2301                                            \n",
       "2302                                            \n",
       "2303                                            \n",
       "\n",
       "                               file_name  \n",
       "0     10.1016@j.biortech.2010.01.041.pdf  \n",
       "1     10.1016@j.biortech.2010.01.041.pdf  \n",
       "2     10.1016@j.biortech.2010.01.041.pdf  \n",
       "3     10.1016@j.biortech.2010.01.041.pdf  \n",
       "4     10.1016@j.biortech.2010.01.041.pdf  \n",
       "...                                  ...  \n",
       "2299   10.1016@S0031-9422(00)94671-5.pdf  \n",
       "2300   10.1016@S0031-9422(00)80444-6.pdf  \n",
       "2301             10.1021@np50032a021.pdf  \n",
       "2302   10.1016@S0031-9422(00)83467-6.pdf  \n",
       "2303    10.1016@0031-9422(80)83208-0.pdf  \n",
       "\n",
       "[2304 rows x 18 columns]"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df = pd.read_parquet('{}file-name_query03-05.parquet'.format(path))\n",
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[446, 34, 116, 52, 6]"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "[len(df.name.unique()), len(df.bioActivity.unique()), len(df.collectionSpecie.unique()), len(df.collectionSite.unique()), len(df.collectionType.unique())]"
   ]
  }
 ],
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