check_data.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "from collections import Counter"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "df = pd.read_csv('evaluation_table.csv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([151714,  35344,   4144, ..., 154251,  14866,   9952])"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df['side effect index (C)'].unique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(924708, 10)"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[('Disorder Lung', 404),\n",
       " ('haemorrhoids', 384),\n",
       " ('angiopathy', 384),\n",
       " ('eruption', 382),\n",
       " ('insomnia', 350),\n",
       " ('bladder retention', 332),\n",
       " ('Hoarseness', 326),\n",
       " ('allergies', 318),\n",
       " ('aspiration pneumonia', 306),\n",
       " ('bundle branch block left', 302),\n",
       " ('abdominal pain upper', 296),\n",
       " ('wheeze', 294),\n",
       " ('hypoxia', 292),\n",
       " ('arterial pressure NOS increased', 292),\n",
       " ('arteriosclerosis', 288),\n",
       " ('haemorrhage rectum', 284),\n",
       " ('mucositis oral', 280),\n",
       " ('Embolism pulmonary', 272),\n",
       " ('alkalosis', 264),\n",
       " ('cellulitis', 262),\n",
       " ('Superficial thrombophlebitis', 262),\n",
       " ('hepatitis', 258),\n",
       " ('stridor', 256),\n",
       " ('Ataxia', 256),\n",
       " ('chronic obstructive airway disease', 248),\n",
       " ('myopia', 248),\n",
       " ('Amnesia', 248),\n",
       " ('blurred vision', 244),\n",
       " ('attempted suicide', 244),\n",
       " ('neumonia', 242)]"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "c = Counter(df[ (df['protein-based prediction']>0.5) & (df['drug-based prediction']<=0.5)]['side effect name'])\n",
    "c.most_common(30)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 60,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>side effect</th>\n",
       "      <th>side effect index (C)</th>\n",
       "      <th>side effect name</th>\n",
       "      <th>drug1</th>\n",
       "      <th>drug1 STITCH (CID)</th>\n",
       "      <th>drug2</th>\n",
       "      <th>drug2 STITCH (CID)</th>\n",
       "      <th>protein-based prediction</th>\n",
       "      <th>drug-based prediction</th>\n",
       "      <th>protein&amp;drug-based prediction</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>234943</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>478</td>\n",
       "      <td>2269</td>\n",
       "      <td>408</td>\n",
       "      <td>3478</td>\n",
       "      <td>0.974980</td>\n",
       "      <td>0.406311</td>\n",
       "      <td>0.649343</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234300</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>408</td>\n",
       "      <td>3478</td>\n",
       "      <td>478</td>\n",
       "      <td>2269</td>\n",
       "      <td>0.974980</td>\n",
       "      <td>0.406311</td>\n",
       "      <td>0.649343</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>233727</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>16</td>\n",
       "      <td>5391</td>\n",
       "      <td>344</td>\n",
       "      <td>4634</td>\n",
       "      <td>0.963967</td>\n",
       "      <td>0.459719</td>\n",
       "      <td>0.815752</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234370</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>344</td>\n",
       "      <td>4634</td>\n",
       "      <td>16</td>\n",
       "      <td>5391</td>\n",
       "      <td>0.963967</td>\n",
       "      <td>0.459719</td>\n",
       "      <td>0.815752</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234457</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>110</td>\n",
       "      <td>2554</td>\n",
       "      <td>49</td>\n",
       "      <td>6398525</td>\n",
       "      <td>0.955052</td>\n",
       "      <td>0.500000</td>\n",
       "      <td>0.692992</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>233814</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>49</td>\n",
       "      <td>6398525</td>\n",
       "      <td>110</td>\n",
       "      <td>2554</td>\n",
       "      <td>0.955052</td>\n",
       "      <td>0.500000</td>\n",
       "      <td>0.692992</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>233700</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>11</td>\n",
       "      <td>5376</td>\n",
       "      <td>236</td>\n",
       "      <td>5732</td>\n",
       "      <td>0.927744</td>\n",
       "      <td>0.500000</td>\n",
       "      <td>0.733398</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234343</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>236</td>\n",
       "      <td>5732</td>\n",
       "      <td>11</td>\n",
       "      <td>5376</td>\n",
       "      <td>0.927744</td>\n",
       "      <td>0.500000</td>\n",
       "      <td>0.733398</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>233838</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>55</td>\n",
       "      <td>4112</td>\n",
       "      <td>123</td>\n",
       "      <td>123620</td>\n",
       "      <td>0.907109</td>\n",
       "      <td>0.479345</td>\n",
       "      <td>0.787080</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234481</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>123</td>\n",
       "      <td>123620</td>\n",
       "      <td>55</td>\n",
       "      <td>4112</td>\n",
       "      <td>0.907109</td>\n",
       "      <td>0.479345</td>\n",
       "      <td>0.787080</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>233720</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>13</td>\n",
       "      <td>5556</td>\n",
       "      <td>173</td>\n",
       "      <td>2118</td>\n",
       "      <td>0.898500</td>\n",
       "      <td>0.445818</td>\n",
       "      <td>0.612275</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234363</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>173</td>\n",
       "      <td>2118</td>\n",
       "      <td>13</td>\n",
       "      <td>5556</td>\n",
       "      <td>0.898500</td>\n",
       "      <td>0.445818</td>\n",
       "      <td>0.612275</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234372</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>446</td>\n",
       "      <td>2477</td>\n",
       "      <td>16</td>\n",
       "      <td>5391</td>\n",
       "      <td>0.895970</td>\n",
       "      <td>0.492663</td>\n",
       "      <td>0.715965</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>233729</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>16</td>\n",
       "      <td>5391</td>\n",
       "      <td>446</td>\n",
       "      <td>2477</td>\n",
       "      <td>0.895970</td>\n",
       "      <td>0.492663</td>\n",
       "      <td>0.715965</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>233978</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>104</td>\n",
       "      <td>4635</td>\n",
       "      <td>408</td>\n",
       "      <td>3478</td>\n",
       "      <td>0.889108</td>\n",
       "      <td>0.500000</td>\n",
       "      <td>0.594871</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234621</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>408</td>\n",
       "      <td>3478</td>\n",
       "      <td>104</td>\n",
       "      <td>4635</td>\n",
       "      <td>0.889108</td>\n",
       "      <td>0.500000</td>\n",
       "      <td>0.594871</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>233805</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>42</td>\n",
       "      <td>3348</td>\n",
       "      <td>233</td>\n",
       "      <td>4253</td>\n",
       "      <td>0.887649</td>\n",
       "      <td>0.500000</td>\n",
       "      <td>0.901331</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234448</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>233</td>\n",
       "      <td>4253</td>\n",
       "      <td>42</td>\n",
       "      <td>3348</td>\n",
       "      <td>0.887649</td>\n",
       "      <td>0.500000</td>\n",
       "      <td>0.901331</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234837</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>339</td>\n",
       "      <td>2749</td>\n",
       "      <td>201</td>\n",
       "      <td>2662</td>\n",
       "      <td>0.886499</td>\n",
       "      <td>0.500000</td>\n",
       "      <td>0.678521</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234194</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>201</td>\n",
       "      <td>2662</td>\n",
       "      <td>339</td>\n",
       "      <td>2749</td>\n",
       "      <td>0.886499</td>\n",
       "      <td>0.500000</td>\n",
       "      <td>0.678521</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>233956</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>91</td>\n",
       "      <td>3958</td>\n",
       "      <td>565</td>\n",
       "      <td>4819</td>\n",
       "      <td>0.876742</td>\n",
       "      <td>0.486279</td>\n",
       "      <td>0.635299</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234599</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>565</td>\n",
       "      <td>4819</td>\n",
       "      <td>91</td>\n",
       "      <td>3958</td>\n",
       "      <td>0.876742</td>\n",
       "      <td>0.486279</td>\n",
       "      <td>0.635299</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234744</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>214</td>\n",
       "      <td>3324</td>\n",
       "      <td>150</td>\n",
       "      <td>450</td>\n",
       "      <td>0.873637</td>\n",
       "      <td>0.397882</td>\n",
       "      <td>0.629676</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234101</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>150</td>\n",
       "      <td>450</td>\n",
       "      <td>214</td>\n",
       "      <td>3324</td>\n",
       "      <td>0.873637</td>\n",
       "      <td>0.397882</td>\n",
       "      <td>0.629676</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234494</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>172</td>\n",
       "      <td>6447131</td>\n",
       "      <td>58</td>\n",
       "      <td>853</td>\n",
       "      <td>0.866638</td>\n",
       "      <td>0.500000</td>\n",
       "      <td>0.706546</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>233851</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>58</td>\n",
       "      <td>853</td>\n",
       "      <td>172</td>\n",
       "      <td>6447131</td>\n",
       "      <td>0.866638</td>\n",
       "      <td>0.500000</td>\n",
       "      <td>0.706546</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234355</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>262</td>\n",
       "      <td>5281104</td>\n",
       "      <td>12</td>\n",
       "      <td>5090</td>\n",
       "      <td>0.856201</td>\n",
       "      <td>0.434637</td>\n",
       "      <td>0.495505</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>233712</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>12</td>\n",
       "      <td>5090</td>\n",
       "      <td>262</td>\n",
       "      <td>5281104</td>\n",
       "      <td>0.856201</td>\n",
       "      <td>0.434637</td>\n",
       "      <td>0.495505</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234784</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>262</td>\n",
       "      <td>5281104</td>\n",
       "      <td>176</td>\n",
       "      <td>3062</td>\n",
       "      <td>0.856040</td>\n",
       "      <td>0.395033</td>\n",
       "      <td>0.515987</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234141</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>176</td>\n",
       "      <td>3062</td>\n",
       "      <td>262</td>\n",
       "      <td>5281104</td>\n",
       "      <td>0.856040</td>\n",
       "      <td>0.395033</td>\n",
       "      <td>0.515987</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>234750</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>400</td>\n",
       "      <td>8953</td>\n",
       "      <td>151</td>\n",
       "      <td>2678</td>\n",
       "      <td>0.684533</td>\n",
       "      <td>0.451933</td>\n",
       "      <td>0.583345</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234107</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>151</td>\n",
       "      <td>2678</td>\n",
       "      <td>400</td>\n",
       "      <td>8953</td>\n",
       "      <td>0.684533</td>\n",
       "      <td>0.451933</td>\n",
       "      <td>0.583345</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234415</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>104</td>\n",
       "      <td>4635</td>\n",
       "      <td>35</td>\n",
       "      <td>3911</td>\n",
       "      <td>0.680462</td>\n",
       "      <td>0.500000</td>\n",
       "      <td>0.660367</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>233772</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>35</td>\n",
       "      <td>3911</td>\n",
       "      <td>104</td>\n",
       "      <td>4635</td>\n",
       "      <td>0.680462</td>\n",
       "      <td>0.500000</td>\n",
       "      <td>0.660367</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234940</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>484</td>\n",
       "      <td>3454</td>\n",
       "      <td>393</td>\n",
       "      <td>2955</td>\n",
       "      <td>0.665288</td>\n",
       "      <td>0.261776</td>\n",
       "      <td>0.497387</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234297</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>393</td>\n",
       "      <td>2955</td>\n",
       "      <td>484</td>\n",
       "      <td>3454</td>\n",
       "      <td>0.665288</td>\n",
       "      <td>0.261776</td>\n",
       "      <td>0.497387</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234738</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>222</td>\n",
       "      <td>5095</td>\n",
       "      <td>145</td>\n",
       "      <td>2022</td>\n",
       "      <td>0.654563</td>\n",
       "      <td>0.359001</td>\n",
       "      <td>0.586087</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234095</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>145</td>\n",
       "      <td>2022</td>\n",
       "      <td>222</td>\n",
       "      <td>5095</td>\n",
       "      <td>0.654563</td>\n",
       "      <td>0.359001</td>\n",
       "      <td>0.586087</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234804</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>309</td>\n",
       "      <td>4585</td>\n",
       "      <td>188</td>\n",
       "      <td>3003</td>\n",
       "      <td>0.643848</td>\n",
       "      <td>0.500000</td>\n",
       "      <td>0.659577</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234161</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>188</td>\n",
       "      <td>3003</td>\n",
       "      <td>309</td>\n",
       "      <td>4585</td>\n",
       "      <td>0.643848</td>\n",
       "      <td>0.500000</td>\n",
       "      <td>0.659577</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234569</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>610</td>\n",
       "      <td>4195</td>\n",
       "      <td>79</td>\n",
       "      <td>4595</td>\n",
       "      <td>0.638207</td>\n",
       "      <td>0.500000</td>\n",
       "      <td>0.518226</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>233926</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>79</td>\n",
       "      <td>4595</td>\n",
       "      <td>610</td>\n",
       "      <td>4195</td>\n",
       "      <td>0.638207</td>\n",
       "      <td>0.500000</td>\n",
       "      <td>0.518226</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234585</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>353</td>\n",
       "      <td>4616</td>\n",
       "      <td>86</td>\n",
       "      <td>60831</td>\n",
       "      <td>0.625898</td>\n",
       "      <td>0.499201</td>\n",
       "      <td>0.516891</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>233942</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>86</td>\n",
       "      <td>60831</td>\n",
       "      <td>353</td>\n",
       "      <td>4616</td>\n",
       "      <td>0.625898</td>\n",
       "      <td>0.499201</td>\n",
       "      <td>0.516891</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234156</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>184</td>\n",
       "      <td>3883</td>\n",
       "      <td>420</td>\n",
       "      <td>5184</td>\n",
       "      <td>0.615045</td>\n",
       "      <td>0.379186</td>\n",
       "      <td>0.472549</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234799</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>420</td>\n",
       "      <td>5184</td>\n",
       "      <td>184</td>\n",
       "      <td>3883</td>\n",
       "      <td>0.615045</td>\n",
       "      <td>0.379186</td>\n",
       "      <td>0.472549</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>233909</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>74</td>\n",
       "      <td>4259</td>\n",
       "      <td>413</td>\n",
       "      <td>581</td>\n",
       "      <td>0.607709</td>\n",
       "      <td>0.431758</td>\n",
       "      <td>0.548025</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234552</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>413</td>\n",
       "      <td>581</td>\n",
       "      <td>74</td>\n",
       "      <td>4259</td>\n",
       "      <td>0.607709</td>\n",
       "      <td>0.431758</td>\n",
       "      <td>0.548025</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>233801</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>41</td>\n",
       "      <td>83786</td>\n",
       "      <td>523</td>\n",
       "      <td>3702</td>\n",
       "      <td>0.599659</td>\n",
       "      <td>0.500000</td>\n",
       "      <td>0.615620</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234444</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>523</td>\n",
       "      <td>3702</td>\n",
       "      <td>41</td>\n",
       "      <td>83786</td>\n",
       "      <td>0.599659</td>\n",
       "      <td>0.500000</td>\n",
       "      <td>0.615620</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234506</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>160</td>\n",
       "      <td>4475485</td>\n",
       "      <td>61</td>\n",
       "      <td>59708</td>\n",
       "      <td>0.576551</td>\n",
       "      <td>0.442407</td>\n",
       "      <td>0.604197</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>233863</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>61</td>\n",
       "      <td>59708</td>\n",
       "      <td>160</td>\n",
       "      <td>4475485</td>\n",
       "      <td>0.576551</td>\n",
       "      <td>0.442407</td>\n",
       "      <td>0.604197</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>233698</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>9</td>\n",
       "      <td>10631</td>\n",
       "      <td>567</td>\n",
       "      <td>3914</td>\n",
       "      <td>0.554112</td>\n",
       "      <td>0.500000</td>\n",
       "      <td>0.680168</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234341</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>567</td>\n",
       "      <td>3914</td>\n",
       "      <td>9</td>\n",
       "      <td>10631</td>\n",
       "      <td>0.554112</td>\n",
       "      <td>0.500000</td>\n",
       "      <td>0.680168</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234416</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>113</td>\n",
       "      <td>3222</td>\n",
       "      <td>35</td>\n",
       "      <td>3911</td>\n",
       "      <td>0.544548</td>\n",
       "      <td>0.500000</td>\n",
       "      <td>0.703025</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>233773</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>35</td>\n",
       "      <td>3911</td>\n",
       "      <td>113</td>\n",
       "      <td>3222</td>\n",
       "      <td>0.544548</td>\n",
       "      <td>0.500000</td>\n",
       "      <td>0.703025</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234678</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>125</td>\n",
       "      <td>2405</td>\n",
       "      <td>118</td>\n",
       "      <td>2909</td>\n",
       "      <td>0.541796</td>\n",
       "      <td>0.389320</td>\n",
       "      <td>0.596189</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234035</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>118</td>\n",
       "      <td>2909</td>\n",
       "      <td>125</td>\n",
       "      <td>2405</td>\n",
       "      <td>0.541796</td>\n",
       "      <td>0.389320</td>\n",
       "      <td>0.596189</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234255</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>280</td>\n",
       "      <td>3367</td>\n",
       "      <td>304</td>\n",
       "      <td>5978</td>\n",
       "      <td>0.530211</td>\n",
       "      <td>0.229956</td>\n",
       "      <td>0.592153</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234898</th>\n",
       "      <td>130</td>\n",
       "      <td>11991</td>\n",
       "      <td>diarrhea</td>\n",
       "      <td>304</td>\n",
       "      <td>5978</td>\n",
       "      <td>280</td>\n",
       "      <td>3367</td>\n",
       "      <td>0.530211</td>\n",
       "      <td>0.229956</td>\n",
       "      <td>0.592153</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>82 rows × 10 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        side effect  side effect index (C) side effect name  drug1  \\\n",
       "234943          130                  11991         diarrhea    478   \n",
       "234300          130                  11991         diarrhea    408   \n",
       "233727          130                  11991         diarrhea     16   \n",
       "234370          130                  11991         diarrhea    344   \n",
       "234457          130                  11991         diarrhea    110   \n",
       "...             ...                    ...              ...    ...   \n",
       "233773          130                  11991         diarrhea     35   \n",
       "234678          130                  11991         diarrhea    125   \n",
       "234035          130                  11991         diarrhea    118   \n",
       "234255          130                  11991         diarrhea    280   \n",
       "234898          130                  11991         diarrhea    304   \n",
       "\n",
       "        drug1 STITCH (CID)  drug2  drug2 STITCH (CID)  \\\n",
       "234943                2269    408                3478   \n",
       "234300                3478    478                2269   \n",
       "233727                5391    344                4634   \n",
       "234370                4634     16                5391   \n",
       "234457                2554     49             6398525   \n",
       "...                    ...    ...                 ...   \n",
       "233773                3911    113                3222   \n",
       "234678                2405    118                2909   \n",
       "234035                2909    125                2405   \n",
       "234255                3367    304                5978   \n",
       "234898                5978    280                3367   \n",
       "\n",
       "        protein-based prediction  drug-based prediction  \\\n",
       "234943                  0.974980               0.406311   \n",
       "234300                  0.974980               0.406311   \n",
       "233727                  0.963967               0.459719   \n",
       "234370                  0.963967               0.459719   \n",
       "234457                  0.955052               0.500000   \n",
       "...                          ...                    ...   \n",
       "233773                  0.544548               0.500000   \n",
       "234678                  0.541796               0.389320   \n",
       "234035                  0.541796               0.389320   \n",
       "234255                  0.530211               0.229956   \n",
       "234898                  0.530211               0.229956   \n",
       "\n",
       "        protein&drug-based prediction  \n",
       "234943                       0.649343  \n",
       "234300                       0.649343  \n",
       "233727                       0.815752  \n",
       "234370                       0.815752  \n",
       "234457                       0.692992  \n",
       "...                               ...  \n",
       "233773                       0.703025  \n",
       "234678                       0.596189  \n",
       "234035                       0.596189  \n",
       "234255                       0.592153  \n",
       "234898                       0.592153  \n",
       "\n",
       "[82 rows x 10 columns]"
      ]
     },
     "execution_count": 60,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_pp = df[ (df['protein-based prediction']>0.5) & (df['drug-based prediction']<=0.5)]\n",
    "df_pp[ df_pp['side effect index (C)']==11991].sort_values('protein-based prediction', ascending=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## GO"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "https://pypi.org/project/goatools/\n",
    "\n",
    "https://www.ncbi.nlm.nih.gov/pubmed/27812946\n",
    "\n",
    "https://nbviewer.jupyter.org/urls/dessimozlab.github.io/go-handbook/GO%20Tutorial%20in%20Python%20-%20Exercises.ipynb\n",
    "https://nbviewer.jupyter.org/urls/dessimozlab.github.io/go-handbook/GO%20Tutorial%20in%20Python%20-%20Solutions.ipynb"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import scipy.sparse as sp"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [],
   "source": [
    "drug_protein = sp.load_npz('./data/sym_adj/drug-protein-sparse-adj.npz')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 49,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(array([ 14,  31,  56,  97, 124, 127, 138, 237, 372, 379, 481, 493, 527,\n",
       "        530, 615]),)"
      ]
     },
     "execution_count": 49,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "np.nonzero(drug_protein.toarray()[:, 9568])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pickle\n",
    "with open('./data/index_map/protein-map.pkl', 'rb') as f:\n",
    "    protein_map = pickle.load(f)\n",
    "\n",
    "    # drug id - index\n",
    "with open('./data/index_map/drug-map.pkl', 'rb') as f:\n",
    "    drug_map = pickle.load(f)\n",
    "inv_drug_map = {v: k for k, v in drug_map.items()}\n",
    "\n",
    "# combo id - index\n",
    "with open('./data/index_map/combo_map.pkl', 'rb') as f:\n",
    "    combo_map = pickle.load(f)\n",
    "inv_combo_map = {v: k for k, v in combo_map.items()}\n",
    "\n",
    "with open('./data/index_map/combo-name-map.pkl', 'rb') as f:\n",
    "    combo_name_map = pickle.load(f)\n",
    "inv_combo_name_map = {v: k for k, v in combo_name_map.items()}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "metadata": {},
   "outputs": [],
   "source": [
    "inv_protein_map = {v:k for k, v in protein_map.items()}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "9568"
      ]
     },
     "execution_count": 48,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "protein_map[1544]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Drug IDs interacting with this protein (9568 = gene ID)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[4946,\n",
       " 4917,\n",
       " 3899,\n",
       " 4485,\n",
       " 271,\n",
       " 4189,\n",
       " 4543,\n",
       " 4499,\n",
       " 3767,\n",
       " 3032,\n",
       " 5472,\n",
       " 3198,\n",
       " 2099,\n",
       " 3117,\n",
       " 4932]"
      ]
     },
     "execution_count": 54,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "[inv_drug_map[i] for i in np.nonzero(drug_protein.toarray()[:, 9568])[0].tolist()]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 55,
   "metadata": {},
   "outputs": [],
   "source": [
    "p_protein = sp.load_npz('./data/sym_adj/protein-sparse-adj.npz')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 56,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[0., 1., 1., ..., 0., 0., 0.],\n",
       "       [1., 0., 0., ..., 0., 0., 0.],\n",
       "       [1., 0., 0., ..., 0., 0., 0.],\n",
       "       ...,\n",
       "       [0., 0., 0., ..., 0., 0., 0.],\n",
       "       [0., 0., 0., ..., 0., 0., 0.],\n",
       "       [0., 0., 0., ..., 0., 0., 0.]])"
      ]
     },
     "execution_count": 56,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "p_protein.toarray()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# GO for human"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## GO: protein"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "import Bio.UniProt.GOA as GOA"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "from ftplib import FTP\n",
    "\n",
    "data_folder = './data'\n",
    "arab_uri = '/pub/databases/GO/goa/HUMAN/goa_human.gaf.gz'\n",
    "arab_fn = arab_uri.split('/')[-1]\n",
    "\n",
    "# Check if the file exists already\n",
    "arab_gaf = os.path.join(data_folder, arab_fn)\n",
    "if(not os.path.isfile(arab_gaf)):\n",
    "    # Login to FTP server\n",
    "    ebi_ftp = FTP('ftp.ebi.ac.uk')\n",
    "    ebi_ftp.login() # Logs in anonymously\n",
    "    \n",
    "    # Download\n",
    "    with open(arab_gaf,'wb') as arab_fp:\n",
    "        ebi_ftp.retrbinary('RETR {}'.format(arab_uri), arab_fp.write)\n",
    "        \n",
    "    # Logout from FTP server\n",
    "    ebi_ftp.quit()\n",
    "    \n",
    "import gzip\n",
    "\n",
    "# File is a gunzip file, so we need to open it in this way\n",
    "with gzip.open(arab_gaf, 'rt') as arab_gaf_fp:\n",
    "    arab_funcs = {}  # Initialise the dictionary of functions\n",
    "    \n",
    "    # Iterate on each function using Bio.UniProt.GOA library.\n",
    "    for entry in GOA.gafiterator(arab_gaf_fp):\n",
    "        uniprot_id = entry.pop('DB_Object_ID')\n",
    "        arab_funcs[uniprot_id] = entry"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "protid = 'P05177'\n",
    "protsym = 'CYP1A2' #CP1A2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[('P05177',\n",
       "  {'Annotation_Extension': '',\n",
       "   'Aspect': 'F',\n",
       "   'Assigned_By': 'UniProt',\n",
       "   'DB': 'UniProtKB',\n",
       "   'DB:Reference': ['PMID:12865317'],\n",
       "   'DB_Object_Name': 'Cytochrome P450 1A2',\n",
       "   'DB_Object_Symbol': 'CYP1A2',\n",
       "   'DB_Object_Type': 'protein',\n",
       "   'Date': '20190412',\n",
       "   'Evidence': 'IDA',\n",
       "   'GO_ID': 'GO:0101021',\n",
       "   'Gene_Product_Form_ID': '',\n",
       "   'Qualifier': [''],\n",
       "   'Synonym': ['CYP1A2'],\n",
       "   'Taxon_ID': ['taxon:9606'],\n",
       "   'With': ['']})]"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "[(ki,vi) for ki,vi in arab_funcs.items() if vi['DB_Object_Symbol']==protsym]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[('P05177',\n",
       "  {'Annotation_Extension': '',\n",
       "   'Aspect': 'F',\n",
       "   'Assigned_By': 'UniProt',\n",
       "   'DB': 'UniProtKB',\n",
       "   'DB:Reference': ['PMID:12865317'],\n",
       "   'DB_Object_Name': 'Cytochrome P450 1A2',\n",
       "   'DB_Object_Symbol': 'CYP1A2',\n",
       "   'DB_Object_Type': 'protein',\n",
       "   'Date': '20190412',\n",
       "   'Evidence': 'IDA',\n",
       "   'GO_ID': 'GO:0101021',\n",
       "   'Gene_Product_Form_ID': '',\n",
       "   'Qualifier': [''],\n",
       "   'Synonym': ['CYP1A2'],\n",
       "   'Taxon_ID': ['taxon:9606'],\n",
       "   'With': ['']})]"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "[(ki,vi) for ki,vi in arab_funcs.items() if ki==protid]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "http://amigo.geneontology.org/amigo/gene_product/UniProtKB:P05177"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## GO: all"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [],
   "source": [
    "import wget,os\n",
    "\n",
    "go_obo_url = 'http://purl.obolibrary.org/obo/go/go-basic.obo'\n",
    "data_folder = os.getcwd() + '/data'\n",
    "\n",
    "# Check if we have the ./data directory already\n",
    "if(not os.path.isfile(data_folder)):\n",
    "    # Emulate mkdir -p (no error if folder exists)\n",
    "    try:\n",
    "        os.mkdir(data_folder)\n",
    "    except OSError as e:\n",
    "        if(e.errno != 17):\n",
    "            raise e\n",
    "else:\n",
    "    raise Exception('Data path (' + data_folder + ') exists as a file. '\n",
    "                   'Please rename, remove or change the desired location of the data path.')\n",
    "\n",
    "# Check if the file exists already\n",
    "if(not os.path.isfile(data_folder+'/go-basic.obo')):\n",
    "    go_obo = wget.download(go_obo_url, data_folder+'/go-basic.obo')\n",
    "else:\n",
    "    go_obo = data_folder+'/go-basic.obo'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/mnt/c/Users/laure/Documents/git/TIP/data/go-basic.obo: fmt(1.2) rel(2019-12-09) 47,311 GO Terms\n"
     ]
    }
   ],
   "source": [
    "# Import the OBO parser from GOATools\n",
    "from goatools import obo_parser\n",
    "\n",
    "go = obo_parser.GODag(go_obo)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'biological_process'"
      ]
     },
     "execution_count": 38,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "kk = go[list(go.keys())[0]]\n",
    "kk.namespace"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "processes = {k:v for k,v in go.items() if v.namespace=='biological_process'}"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### For each process, get the set of proteins (genes)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "metadata": {},
   "outputs": [],
   "source": [
    "# processes"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Utility/significance of explaining\n",
    "- know mechanism, can predict triple/higher-order side effects\n",
    "    - other drugs affecting the same (GO) processes\n",
    "- help design new polypharmacy treatment to counter the side effect"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Software availability\n",
    "- module\n",
    "- Biopython accesses our module's API (contribute to Biopython)\n"
   ]
  }
 ],
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