greengamma/examples/repurposing_by_gene.ipynb

{
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  {
   "cell_type": "markdown",
   "metadata": {
    "deletable": true,
    "editable": true
   },
   "source": [
    "# Repurposing by gene"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false,
    "deletable": true,
    "editable": true
   },
   "outputs": [],
   "source": [
    "#To make nicer looking outputs\n",
    "from IPython.core.display import display, HTML\n",
    "import requests\n",
    "\n",
    "#Load some functions for parsing quick output\n",
    "import os\n",
    "import sys\n",
    "module_path = os.path.abspath(os.path.join('..'))\n",
    "if module_path not in sys.path:\n",
    "    sys.path.append(module_path)\n",
    "from gg_functions import parse_answer, get_view_url\n",
    "\n",
    "robokop='robokop.renci.org'\n",
    "\n",
    "from disease_lists import rare_diseases, common_diseases\n",
    "diseases = rare_diseases + common_diseases"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false,
    "deletable": true,
    "editable": true,
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<h3>arthritis</h3>"
      ],
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       "<a href=http://robokop.renci.org/simple/view/91c6505b-dd6e-4599-b916-578c8640809b>View Answer in ROBOKOP</a>"
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      "text/plain": [
       "<IPython.core.display.HTML object>"
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       "<div>\n",
       "<style>\n",
       "    .dataframe thead tr:only-child th {\n",
       "        text-align: right;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: left;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>n1 - id</th>\n",
       "      <th>n1 - name</th>\n",
       "      <th>n2 - id</th>\n",
       "      <th>n2 - name</th>\n",
       "      <th>n3 - id</th>\n",
       "      <th>n3 - name</th>\n",
       "      <th>score</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>HGNC:12679</td>\n",
       "      <td>VDR</td>\n",
       "      <td>MONDO:0005520</td>\n",
       "      <td>rickets (disease)</td>\n",
       "      <td>CHEBI:17823</td>\n",
       "      <td>calcitriol</td>\n",
       "      <td>1.644453</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>HGNC:870</td>\n",
       "      <td>ATP7B</td>\n",
       "      <td>MONDO:0010200</td>\n",
       "      <td>Wilson disease</td>\n",
       "      <td>CHEBI:28694</td>\n",
       "      <td>copper atom</td>\n",
       "      <td>1.495524</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>HGNC:6081</td>\n",
       "      <td>INS</td>\n",
       "      <td>MONDO:0004946</td>\n",
       "      <td>hypoglycemia</td>\n",
       "      <td>CHEBI:17234</td>\n",
       "      <td>glucose</td>\n",
       "      <td>1.372602</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>HGNC:1884</td>\n",
       "      <td>CFTR</td>\n",
       "      <td>MONDO:0009061</td>\n",
       "      <td>cystic fibrosis</td>\n",
       "      <td>CHEBI:66901</td>\n",
       "      <td>ivacaftor</td>\n",
       "      <td>1.342034</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>HGNC:4932</td>\n",
       "      <td>HLA-B</td>\n",
       "      <td>MONDO:0002144</td>\n",
       "      <td>hyperuricemia (disease)</td>\n",
       "      <td>CHEBI:40279</td>\n",
       "      <td>allopurinol</td>\n",
       "      <td>1.258657</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     n1 - id  n1 - name        n2 - id                n2 - name      n3 - id   \\\n",
       "0  HGNC:12679        VDR  MONDO:0005520        rickets (disease)  CHEBI:17823   \n",
       "1    HGNC:870      ATP7B  MONDO:0010200           Wilson disease  CHEBI:28694   \n",
       "2   HGNC:6081        INS  MONDO:0004946             hypoglycemia  CHEBI:17234   \n",
       "3   HGNC:1884       CFTR  MONDO:0009061          cystic fibrosis  CHEBI:66901   \n",
       "4   HGNC:4932      HLA-B  MONDO:0002144  hyperuricemia (disease)  CHEBI:40279   \n",
       "\n",
       "    n3 - name      score  \n",
       "0   calcitriol  1.644453  \n",
       "1  copper atom  1.495524  \n",
       "2      glucose  1.372602  \n",
       "3    ivacaftor  1.342034  \n",
       "4  allopurinol  1.258657  "
      ]
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     "metadata": {},
     "output_type": "display_data"
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     "data": {
      "text/html": [
       "<h3>type 2 diabetes mellitus</h3>"
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       "      <th>n2 - id</th>\n",
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       "      <th>n3 - id</th>\n",
       "      <th>n3 - name</th>\n",
       "      <th>score</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>HGNC:6081</td>\n",
       "      <td>INS</td>\n",
       "      <td>MONDO:0004946</td>\n",
       "      <td>hypoglycemia</td>\n",
       "      <td>CHEBI:17234</td>\n",
       "      <td>glucose</td>\n",
       "      <td>2.046613</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>HGNC:11621</td>\n",
       "      <td>HNF1A</td>\n",
       "      <td>MONDO:0004946</td>\n",
       "      <td>hypoglycemia</td>\n",
       "      <td>CHEBI:17234</td>\n",
       "      <td>glucose</td>\n",
       "      <td>2.034507</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>HGNC:11006</td>\n",
       "      <td>SLC2A2</td>\n",
       "      <td>MONDO:0004946</td>\n",
       "      <td>hypoglycemia</td>\n",
       "      <td>CHEBI:17234</td>\n",
       "      <td>glucose</td>\n",
       "      <td>1.964184</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>HGNC:9232</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>MONDO:0004946</td>\n",
       "      <td>hypoglycemia</td>\n",
       "      <td>CHEBI:17234</td>\n",
       "      <td>glucose</td>\n",
       "      <td>1.961608</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>HGNC:6091</td>\n",
       "      <td>INSR</td>\n",
       "      <td>MONDO:0004946</td>\n",
       "      <td>hypoglycemia</td>\n",
       "      <td>CHEBI:17234</td>\n",
       "      <td>glucose</td>\n",
       "      <td>1.899160</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
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       "     n1 - id  n1 - name        n2 - id     n2 - name      n3 - id  n3 - name   \\\n",
       "0   HGNC:6081        INS  MONDO:0004946  hypoglycemia  CHEBI:17234    glucose   \n",
       "1  HGNC:11621      HNF1A  MONDO:0004946  hypoglycemia  CHEBI:17234    glucose   \n",
       "2  HGNC:11006     SLC2A2  MONDO:0004946  hypoglycemia  CHEBI:17234    glucose   \n",
       "3   HGNC:9232      PPARA  MONDO:0004946  hypoglycemia  CHEBI:17234    glucose   \n",
       "4   HGNC:6091       INSR  MONDO:0004946  hypoglycemia  CHEBI:17234    glucose   \n",
       "\n",
       "      score  \n",
       "0  2.046613  \n",
       "1  2.034507  \n",
       "2  1.964184  \n",
       "3  1.961608  \n",
       "4  1.899160  "
      ]
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     "metadata": {},
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     "data": {
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       "<h3>dermatitis</h3>"
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       "  <thead>\n",
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       "      <th>n1 - id</th>\n",
       "      <th>n1 - name</th>\n",
       "      <th>n2 - id</th>\n",
       "      <th>n2 - name</th>\n",
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       "      <th>n3 - name</th>\n",
       "      <th>score</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>HGNC:4932</td>\n",
       "      <td>HLA-B</td>\n",
       "      <td>MONDO:0002144</td>\n",
       "      <td>hyperuricemia (disease)</td>\n",
       "      <td>CHEBI:40279</td>\n",
       "      <td>allopurinol</td>\n",
       "      <td>1.381769</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>HGNC:17129</td>\n",
       "      <td>SLC39A4</td>\n",
       "      <td>MONDO:0006523</td>\n",
       "      <td>acrodermatitis</td>\n",
       "      <td>CHEBI:27363</td>\n",
       "      <td>zinc atom</td>\n",
       "      <td>1.379584</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>HGNC:11364</td>\n",
       "      <td>STAT3</td>\n",
       "      <td>MONDO:0005311</td>\n",
       "      <td>atherosclerosis</td>\n",
       "      <td>CHEBI:16243</td>\n",
       "      <td>quercetin</td>\n",
       "      <td>1.206149</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>HGNC:11364</td>\n",
       "      <td>STAT3</td>\n",
       "      <td>MONDO:0021040</td>\n",
       "      <td>pancreatic neoplasm</td>\n",
       "      <td>CHEBI:175901</td>\n",
       "      <td>gemcitabine</td>\n",
       "      <td>1.149370</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>HGNC:812</td>\n",
       "      <td>ATP2A2</td>\n",
       "      <td>MONDO:0005252</td>\n",
       "      <td>heart failure</td>\n",
       "      <td>CHEBI:3441</td>\n",
       "      <td>carvedilol</td>\n",
       "      <td>1.127502</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     n1 - id  n1 - name        n2 - id                n2 - name   \\\n",
       "0   HGNC:4932      HLA-B  MONDO:0002144  hyperuricemia (disease)   \n",
       "1  HGNC:17129    SLC39A4  MONDO:0006523           acrodermatitis   \n",
       "2  HGNC:11364      STAT3  MONDO:0005311          atherosclerosis   \n",
       "3  HGNC:11364      STAT3  MONDO:0021040      pancreatic neoplasm   \n",
       "4    HGNC:812     ATP2A2  MONDO:0005252            heart failure   \n",
       "\n",
       "       n3 - id    n3 - name      score  \n",
       "0   CHEBI:40279  allopurinol  1.381769  \n",
       "1   CHEBI:27363    zinc atom  1.379584  \n",
       "2   CHEBI:16243    quercetin  1.206149  \n",
       "3  CHEBI:175901  gemcitabine  1.149370  \n",
       "4    CHEBI:3441   carvedilol  1.127502  "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
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     "data": {
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       "<h3>rheumatoid arthritis</h3>"
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       "    .dataframe thead tr:only-child th {\n",
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       "    .dataframe thead th {\n",
       "        text-align: left;\n",
       "    }\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>n1 - id</th>\n",
       "      <th>n1 - name</th>\n",
       "      <th>n2 - id</th>\n",
       "      <th>n2 - name</th>\n",
       "      <th>n3 - id</th>\n",
       "      <th>n3 - name</th>\n",
       "      <th>score</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>HGNC:12679</td>\n",
       "      <td>VDR</td>\n",
       "      <td>MONDO:0005520</td>\n",
       "      <td>rickets (disease)</td>\n",
       "      <td>CHEBI:17823</td>\n",
       "      <td>calcitriol</td>\n",
       "      <td>1.574685</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>HGNC:9204</td>\n",
       "      <td>PON1</td>\n",
       "      <td>MONDO:0005542</td>\n",
       "      <td>acute coronary syndrome</td>\n",
       "      <td>CHEBI:37941</td>\n",
       "      <td>clopidogrel</td>\n",
       "      <td>1.335445</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>HGNC:53</td>\n",
       "      <td>ABCC2</td>\n",
       "      <td>MONDO:0005388</td>\n",
       "      <td>primary biliary cholangitis</td>\n",
       "      <td>CHEBI:9907</td>\n",
       "      <td>ursodeoxycholic acid</td>\n",
       "      <td>1.290341</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>HGNC:4932</td>\n",
       "      <td>HLA-B</td>\n",
       "      <td>MONDO:0002144</td>\n",
       "      <td>hyperuricemia (disease)</td>\n",
       "      <td>CHEBI:40279</td>\n",
       "      <td>allopurinol</td>\n",
       "      <td>1.241002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>HGNC:12680</td>\n",
       "      <td>VEGFA</td>\n",
       "      <td>MONDO:0005311</td>\n",
       "      <td>atherosclerosis</td>\n",
       "      <td>CHEBI:16243</td>\n",
       "      <td>quercetin</td>\n",
       "      <td>1.219089</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
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      ],
      "text/plain": [
       "     n1 - id  n1 - name        n2 - id                    n2 - name   \\\n",
       "0  HGNC:12679        VDR  MONDO:0005520            rickets (disease)   \n",
       "1   HGNC:9204       PON1  MONDO:0005542      acute coronary syndrome   \n",
       "2     HGNC:53      ABCC2  MONDO:0005388  primary biliary cholangitis   \n",
       "3   HGNC:4932      HLA-B  MONDO:0002144      hyperuricemia (disease)   \n",
       "4  HGNC:12680      VEGFA  MONDO:0005311              atherosclerosis   \n",
       "\n",
       "      n3 - id             n3 - name      score  \n",
       "0  CHEBI:17823            calcitriol  1.574685  \n",
       "1  CHEBI:37941           clopidogrel  1.335445  \n",
       "2   CHEBI:9907  ursodeoxycholic acid  1.290341  \n",
       "3  CHEBI:40279           allopurinol  1.241002  \n",
       "4  CHEBI:16243             quercetin  1.219089  "
      ]
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     "output_type": "display_data"
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       "      <td>HGNC:53</td>\n",
       "      <td>ABCC2</td>\n",
       "      <td>MONDO:0005388</td>\n",
       "      <td>primary biliary cholangitis</td>\n",
       "      <td>CHEBI:9907</td>\n",
       "      <td>ursodeoxycholic acid</td>\n",
       "      <td>1.345748</td>\n",
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       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>HGNC:5464</td>\n",
       "      <td>IGF1</td>\n",
       "      <td>MONDO:0001119</td>\n",
       "      <td>premature menopause</td>\n",
       "      <td>CHEBI:17347</td>\n",
       "      <td>testosterone</td>\n",
       "      <td>1.337890</td>\n",
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       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>HGNC:9232</td>\n",
       "      <td>PPARA</td>\n",
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       "      <td>hypoglycemia</td>\n",
       "      <td>CHEBI:17234</td>\n",
       "      <td>glucose</td>\n",
       "      <td>1.326610</td>\n",
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       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>HGNC:4623</td>\n",
       "      <td>GSR</td>\n",
       "      <td>MONDO:0004946</td>\n",
       "      <td>hypoglycemia</td>\n",
       "      <td>CHEBI:17234</td>\n",
       "      <td>glucose</td>\n",
       "      <td>1.293344</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>HGNC:2631</td>\n",
       "      <td>CYP2E1</td>\n",
       "      <td>MONDO:0002046</td>\n",
       "      <td>alcohol abuse</td>\n",
       "      <td>CHEBI:4659</td>\n",
       "      <td>disulfiram</td>\n",
       "      <td>1.289183</td>\n",
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       "0    HGNC:53      ABCC2  MONDO:0005388  primary biliary cholangitis   \n",
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       "2  HGNC:9232      PPARA  MONDO:0004946                 hypoglycemia   \n",
       "3  HGNC:4623        GSR  MONDO:0004946                 hypoglycemia   \n",
       "4  HGNC:2631     CYP2E1  MONDO:0002046                alcohol abuse   \n",
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       "      <td>CHEBI:50122</td>\n",
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       "      <th>0</th>\n",
       "      <td>HGNC:12679</td>\n",
       "      <td>VDR</td>\n",
       "      <td>MONDO:0005520</td>\n",
       "      <td>rickets (disease)</td>\n",
       "      <td>CHEBI:17823</td>\n",
       "      <td>calcitriol</td>\n",
       "      <td>1.427723</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>HGNC:1884</td>\n",
       "      <td>CFTR</td>\n",
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       "      <td>1.409275</td>\n",
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       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>HGNC:12680</td>\n",
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       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>HGNC:4932</td>\n",
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       "      <td>1.311589</td>\n",
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       "      <th>2</th>\n",
       "      <td>HGNC:12679</td>\n",
       "      <td>VDR</td>\n",
       "      <td>MONDO:0007008</td>\n",
       "      <td>uremia</td>\n",
       "      <td>CHEBI:17823</td>\n",
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       "      <td>1.249197</td>\n",
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       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>HGNC:12679</td>\n",
       "      <td>VDR</td>\n",
       "      <td>MONDO:0005520</td>\n",
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       "      <td>CHEBI:31186</td>\n",
       "      <td>alfacalcidol</td>\n",
       "      <td>1.212373</td>\n",
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       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>HGNC:11364</td>\n",
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       "      <td>CHEBI:16243</td>\n",
       "      <td>quercetin</td>\n",
       "      <td>1.211765</td>\n",
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       "0                        rickets (disease)  CHEBI:17823    calcitriol   \n",
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       "      <td>pulmonary arterial hypertension</td>\n",
       "      <td>CHEBI:84879</td>\n",
       "      <td>nitroxyl</td>\n",
       "      <td>1.032412</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>HGNC:1527</td>\n",
       "      <td>CAV1</td>\n",
       "      <td>MONDO:0005252</td>\n",
       "      <td>heart failure</td>\n",
       "      <td>CHEBI:7596</td>\n",
       "      <td>nitroprusside</td>\n",
       "      <td>0.961401</td>\n",
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       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>HGNC:1527</td>\n",
       "      <td>CAV1</td>\n",
       "      <td>MONDO:0015924</td>\n",
       "      <td>pulmonary arterial hypertension</td>\n",
       "      <td>CHEBI:7596</td>\n",
       "      <td>nitroprusside</td>\n",
       "      <td>0.837900</td>\n",
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       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>HGNC:3796</td>\n",
       "      <td>FOS</td>\n",
       "      <td>MONDO:0002125</td>\n",
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       "      <td>CHEBI:7983</td>\n",
       "      <td>pentobarbital</td>\n",
       "      <td>0.813781</td>\n",
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       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>HGNC:1527</td>\n",
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       "      <td>CHEBI:50122</td>\n",
       "      <td>rosiglitazone</td>\n",
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       "0  HGNC:1527       CAV1  MONDO:0015924  pulmonary arterial hypertension   \n",
       "1  HGNC:1527       CAV1  MONDO:0005252                    heart failure   \n",
       "2  HGNC:1527       CAV1  MONDO:0015924  pulmonary arterial hypertension   \n",
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       "4  HGNC:1527       CAV1  MONDO:0001076              glucose intolerance   \n",
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       "0  CHEBI:84879       nitroxyl  1.032412  \n",
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       "2   CHEBI:7596  nitroprusside  0.837900  \n",
       "3   CHEBI:7983  pentobarbital  0.813781  \n",
       "4  CHEBI:50122  rosiglitazone  0.811598  "
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       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>HGNC:11621</td>\n",
       "      <td>HNF1A</td>\n",
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       "      <td>hypoglycemia</td>\n",
       "      <td>CHEBI:17234</td>\n",
       "      <td>glucose</td>\n",
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       "      <td>HGNC:6257</td>\n",
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       "      <th>0</th>\n",
       "      <td>HGNC:4932</td>\n",
       "      <td>HLA-B</td>\n",
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       "      <td>hyperuricemia (disease)</td>\n",
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       "      <td>HGNC:11920</td>\n",
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       "      <td>HGNC:5962</td>\n",
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       "      <td>colitis (disease)</td>\n",
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       "3   CHEBI:3699    cimetidine  1.004823  \n",
       "4  CHEBI:59560   sapropterin  0.997700  "
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       "3   HGNC:9817      RAD51  MONDO:0018881  myelodysplastic syndrome   \n",
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       "      n3 - id               n3 - name      score  \n",
       "0   CHEBI:4450            desmopressin  1.008989  \n",
       "1   CHEBI:3011              benazepril  0.966650  \n",
       "2   CHEBI:4450            desmopressin  0.959465  \n",
       "3  CHEBI:50131  5-aza-2'-deoxycytidine  0.925555  \n",
       "4  CHEBI:28694             copper atom  0.925406  "
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       "      <th>0</th>\n",
       "      <td>HGNC:2295</td>\n",
       "      <td>CP</td>\n",
       "      <td>MONDO:0010200</td>\n",
       "      <td>Wilson disease</td>\n",
       "      <td>CHEBI:28694</td>\n",
       "      <td>copper atom</td>\n",
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       "      <td>HGNC:10908</td>\n",
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       "      <td>HGNC:1527</td>\n",
       "      <td>CAV1</td>\n",
       "      <td>MONDO:0015924</td>\n",
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       "      <td>CHEBI:84879</td>\n",
       "      <td>nitroxyl</td>\n",
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       "      <td>0.941227</td>\n",
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       "      <td>HGNC:3796</td>\n",
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       "      <td>CHEBI:7983</td>\n",
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       "      <td>0.813781</td>\n",
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       "2  HGNC:3796        FOS  MONDO:0002125               status epilepticus   \n",
       "3  HGNC:1527       CAV1  MONDO:0001076              glucose intolerance   \n",
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       "      <td>HGNC:4177</td>\n",
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       "2   HGNC:9449       PRNP  MONDO:0010200            Wilson disease   \n",
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       "2  HGNC:7218        MPO  MONDO:0005203  ischemia reperfusion injury   \n",
       "3  HGNC:7218        MPO  MONDO:0005203  ischemia reperfusion injury   \n",
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       "2   CHEBI:3374           capsaicin  0.792077  \n",
       "3  CHEBI:16236             ethanol  0.778049  \n",
       "4  CHEBI:29150  orthoperiodic acid  0.773134  "
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       "      <td>atrial fibrillation (disease)</td>\n",
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       "      <td>quinidine</td>\n",
       "      <td>1.356835</td>\n",
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       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>HGNC:10593</td>\n",
       "      <td>SCN5A</td>\n",
       "      <td>MONDO:0004981</td>\n",
       "      <td>atrial fibrillation (disease)</td>\n",
       "      <td>CHEBI:75984</td>\n",
       "      <td>flecainide</td>\n",
       "      <td>1.276625</td>\n",
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       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>HGNC:1884</td>\n",
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       "      <td>1.258840</td>\n",
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       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>HGNC:10593</td>\n",
       "      <td>SCN5A</td>\n",
       "      <td>MONDO:0004981</td>\n",
       "      <td>atrial fibrillation (disease)</td>\n",
       "      <td>CHEBI:63619</td>\n",
       "      <td>propafenone</td>\n",
       "      <td>1.249718</td>\n",
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       "0    HGNC:869      ATP7A  MONDO:0010651                 Menkes disease   \n",
       "1  HGNC:10593      SCN5A  MONDO:0004981  atrial fibrillation (disease)   \n",
       "2  HGNC:10593      SCN5A  MONDO:0004981  atrial fibrillation (disease)   \n",
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       "      <td>carmustine</td>\n",
       "      <td>0.867883</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>HGNC:4641</td>\n",
       "      <td>GSTT1</td>\n",
       "      <td>MONDO:0009693</td>\n",
       "      <td>multiple myeloma</td>\n",
       "      <td>CHEBI:28901</td>\n",
       "      <td>busulfan</td>\n",
       "      <td>0.770532</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
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       "1  HGNC:4641      GSTT1  MONDO:0009693  multiple myeloma   CHEBI:3423   \n",
       "2  HGNC:4641      GSTT1  MONDO:0009693  multiple myeloma  CHEBI:24261   \n",
       "3  HGNC:4641      GSTT1  MONDO:0005615      plasmacytoma   CHEBI:3423   \n",
       "4  HGNC:4641      GSTT1  MONDO:0009693  multiple myeloma  CHEBI:28901   \n",
       "\n",
       "       n3 - name      score  \n",
       "0      carmustine  0.989428  \n",
       "1      carmustine  0.956772  \n",
       "2  glucocorticoid  0.870156  \n",
       "3      carmustine  0.867883  \n",
       "4        busulfan  0.770532  "
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       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>HGNC:6081</td>\n",
       "      <td>INS</td>\n",
       "      <td>MONDO:0004946</td>\n",
       "      <td>hypoglycemia</td>\n",
       "      <td>CHEBI:17234</td>\n",
       "      <td>glucose</td>\n",
       "      <td>1.863937</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>HGNC:620</td>\n",
       "      <td>APP</td>\n",
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       "      <td>palsy</td>\n",
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       "      <td>HGNC:427</td>\n",
       "      <td>ALK</td>\n",
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       "      <td>1.516565</td>\n",
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       "  <tbody>\n",
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       "      <th>0</th>\n",
       "      <td>HGNC:2264</td>\n",
       "      <td>COX17</td>\n",
       "      <td>MONDO:0010651</td>\n",
       "      <td>Menkes disease</td>\n",
       "      <td>CHEBI:28694</td>\n",
       "      <td>copper atom</td>\n",
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       "      <td>HGNC:7455</td>\n",
       "      <td>MT-ND1</td>\n",
       "      <td>MONDO:0000190</td>\n",
       "      <td>ventricular fibrillation (disease)</td>\n",
       "      <td>CHEBI:16238</td>\n",
       "      <td>FAD</td>\n",
       "      <td>0.611330</td>\n",
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       "      <th>2</th>\n",
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       "3  CHEBI:28694   copper atom  0.598160  \n",
       "4  CHEBI:46372  ubiquinone-2  0.589755  "
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       "      <td>HGNC:3689</td>\n",
       "      <td>FGFR2</td>\n",
       "      <td>MONDO:0001243</td>\n",
       "      <td>disseminated intravascular coagulation</td>\n",
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       "      <td>HGNC:3689</td>\n",
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       "3                            plasmacytoma  CHEBI:45906   \n",
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       "\n",
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       "0                  Heparin  0.873316  \n",
       "1  reactive oxygen species  0.826125  \n",
       "2                  suramin  0.807957  \n",
       "3                  suramin  0.696416  \n",
       "4       orthoperiodic acid  0.678824  "
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       "      <td>MONDO:0003019</td>\n",
       "      <td>hypokalemia (disease)</td>\n",
       "      <td>CHEBI:9241</td>\n",
       "      <td>spironolactone</td>\n",
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       "3   HGNC:399        ALB  MONDO:0021187  hyperlipidemia (disease)   CHEBI:3750   \n",
       "4  HGNC:2201     COL3A1  MONDO:0003019     hypokalemia (disease)   CHEBI:9241   \n",
       "\n",
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       "2       quercetin  0.812214  \n",
       "3      clofibrate  0.810096  \n",
       "4  spironolactone  0.797432  "
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       "2   HGNC:795        ATM  MONDO:0005615              plasmacytoma  CHEBI:52717   \n",
       "3  HGNC:2295         CP  MONDO:0010200            Wilson disease  CHEBI:28694   \n",
       "4   HGNC:620        APP  MONDO:0006496                     palsy  CHEBI:28694   \n",
       "\n",
       "               n3 - name      score  \n",
       "0              eliglustat  1.083114  \n",
       "1  5-aza-2'-deoxycytidine  1.059473  \n",
       "2              bortezomib  1.032659  \n",
       "3             copper atom  1.002359  \n",
       "4             copper atom  0.977084  "
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       "      <th>score</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>HGNC:4261</td>\n",
       "      <td>GH1</td>\n",
       "      <td>MONDO:0019933</td>\n",
       "      <td>acromegaly</td>\n",
       "      <td>CHEMBL:CHEMBL1680</td>\n",
       "      <td>OCTREOTIDE</td>\n",
       "      <td>1.524126</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>HGNC:4261</td>\n",
       "      <td>GH1</td>\n",
       "      <td>MONDO:0019933</td>\n",
       "      <td>acromegaly</td>\n",
       "      <td>CHEBI:3181</td>\n",
       "      <td>bromocriptine</td>\n",
       "      <td>1.363182</td>\n",
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       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>HGNC:4261</td>\n",
       "      <td>GH1</td>\n",
       "      <td>MONDO:0006373</td>\n",
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       "      <td>1.242924</td>\n",
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       "      <th>3</th>\n",
       "      <td>HGNC:9445</td>\n",
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       "      <td>MONDO:0010911</td>\n",
       "      <td>prolactin-producing pituitary gland adenoma</td>\n",
       "      <td>CHEBI:3181</td>\n",
       "      <td>bromocriptine</td>\n",
       "      <td>1.179609</td>\n",
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       "      <th>4</th>\n",
       "      <td>HGNC:9445</td>\n",
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       "      <td>MONDO:0005804</td>\n",
       "      <td>hyperprolactinemia (disease)</td>\n",
       "      <td>CHEBI:3181</td>\n",
       "      <td>bromocriptine</td>\n",
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       "      <td>HGNC:634</td>\n",
       "      <td>AQP2</td>\n",
       "      <td>MONDO:0000022</td>\n",
       "      <td>nocturnal enuresis</td>\n",
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       "1   HGNC:795        ATM  MONDO:0005615              plasmacytoma  CHEBI:52717   \n",
       "2   HGNC:795        ATM  MONDO:0018881  myelodysplastic syndrome  CHEBI:50131   \n",
       "3   HGNC:795        ATM  MONDO:0018876      mantle cell lymphoma  CHEBI:52717   \n",
       "4  HGNC:1884       CFTR  MONDO:0002909             hyperglycemia   CHEBI:5441   \n",
       "\n",
       "               n3 - name      score  \n",
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       "1              bortezomib  1.184984  \n",
       "2  5-aza-2'-deoxycytidine  1.145690  \n",
       "3              bortezomib  1.097265  \n",
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       "      <th>0</th>\n",
       "      <td>HGNC:14581</td>\n",
       "      <td>PINK1</td>\n",
       "      <td>MONDO:0021095</td>\n",
       "      <td>parkinsonian disorder</td>\n",
       "      <td>CHEBI:15765</td>\n",
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       "      <td>HGNC:7559</td>\n",
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       "      <td>CHEBI:3011</td>\n",
       "      <td>benazepril</td>\n",
       "      <td>1.032061</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>HGNC:620</td>\n",
       "      <td>APP</td>\n",
       "      <td>MONDO:0006496</td>\n",
       "      <td>palsy</td>\n",
       "      <td>CHEBI:28694</td>\n",
       "      <td>copper atom</td>\n",
       "      <td>1.013211</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>HGNC:1033</td>\n",
       "      <td>BDNF</td>\n",
       "      <td>MONDO:0008114</td>\n",
       "      <td>obsessive-compulsive disorder</td>\n",
       "      <td>CHEBI:86990</td>\n",
       "      <td>N-methyl-3-phenyl-3-[4-(trifluoromethyl)phenox...</td>\n",
       "      <td>0.961671</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>HGNC:2707</td>\n",
       "      <td>ACE</td>\n",
       "      <td>MONDO:0005016</td>\n",
       "      <td>diabetic nephropathy</td>\n",
       "      <td>CHEBI:4784</td>\n",
       "      <td>enalapril</td>\n",
       "      <td>0.954259</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    n1 - id  n1 - name        n2 - id                      n2 - name   \\\n",
       "0  HGNC:6081        INS  MONDO:0004946                   hypoglycemia   \n",
       "1  HGNC:2707        ACE  MONDO:0005016           diabetic nephropathy   \n",
       "2   HGNC:620        APP  MONDO:0006496                          palsy   \n",
       "3  HGNC:1033       BDNF  MONDO:0008114  obsessive-compulsive disorder   \n",
       "4  HGNC:2707        ACE  MONDO:0005016           diabetic nephropathy   \n",
       "\n",
       "      n3 - id                                          n3 - name      score  \n",
       "0  CHEBI:17234                                            glucose  1.236224  \n",
       "1   CHEBI:3011                                         benazepril  1.032061  \n",
       "2  CHEBI:28694                                        copper atom  1.013211  \n",
       "3  CHEBI:86990  N-methyl-3-phenyl-3-[4-(trifluoromethyl)phenox...  0.961671  \n",
       "4   CHEBI:4784                                          enalapril  0.954259  "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<h3>combined pituitary hormone deficiencies, genet...</h3>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<a href=http://robokop.renci.org/simple/view/586451fd-48ff-4e28-8767-8500f1823b01>View Answer in ROBOKOP</a>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style>\n",
       "    .dataframe thead tr:only-child th {\n",
       "        text-align: right;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: left;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>n1 - id</th>\n",
       "      <th>n1 - name</th>\n",
       "      <th>n2 - id</th>\n",
       "      <th>n2 - name</th>\n",
       "      <th>n3 - id</th>\n",
       "      <th>n3 - name</th>\n",
       "      <th>score</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>HGNC:4261</td>\n",
       "      <td>GH1</td>\n",
       "      <td>MONDO:0019933</td>\n",
       "      <td>acromegaly</td>\n",
       "      <td>CHEMBL:CHEMBL1680</td>\n",
       "      <td>OCTREOTIDE</td>\n",
       "      <td>1.524126</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>HGNC:4261</td>\n",
       "      <td>GH1</td>\n",
       "      <td>MONDO:0019933</td>\n",
       "      <td>acromegaly</td>\n",
       "      <td>CHEBI:3181</td>\n",
       "      <td>bromocriptine</td>\n",
       "      <td>1.363182</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>HGNC:4261</td>\n",
       "      <td>GH1</td>\n",
       "      <td>MONDO:0006373</td>\n",
       "      <td>pituitary gland adenoma</td>\n",
       "      <td>CHEMBL:CHEMBL1680</td>\n",
       "      <td>OCTREOTIDE</td>\n",
       "      <td>1.242924</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>HGNC:9445</td>\n",
       "      <td>PRL</td>\n",
       "      <td>MONDO:0010911</td>\n",
       "      <td>prolactin-producing pituitary gland adenoma</td>\n",
       "      <td>CHEBI:3181</td>\n",
       "      <td>bromocriptine</td>\n",
       "      <td>1.179609</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>HGNC:9445</td>\n",
       "      <td>PRL</td>\n",
       "      <td>MONDO:0005804</td>\n",
       "      <td>hyperprolactinemia (disease)</td>\n",
       "      <td>CHEBI:3181</td>\n",
       "      <td>bromocriptine</td>\n",
       "      <td>1.155644</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    n1 - id  n1 - name        n2 - id   \\\n",
       "0  HGNC:4261        GH1  MONDO:0019933   \n",
       "1  HGNC:4261        GH1  MONDO:0019933   \n",
       "2  HGNC:4261        GH1  MONDO:0006373   \n",
       "3  HGNC:9445        PRL  MONDO:0010911   \n",
       "4  HGNC:9445        PRL  MONDO:0005804   \n",
       "\n",
       "                                    n2 - name            n3 - id   \\\n",
       "0                                   acromegaly  CHEMBL:CHEMBL1680   \n",
       "1                                   acromegaly         CHEBI:3181   \n",
       "2                      pituitary gland adenoma  CHEMBL:CHEMBL1680   \n",
       "3  prolactin-producing pituitary gland adenoma         CHEBI:3181   \n",
       "4                 hyperprolactinemia (disease)         CHEBI:3181   \n",
       "\n",
       "      n3 - name      score  \n",
       "0     OCTREOTIDE  1.524126  \n",
       "1  bromocriptine  1.363182  \n",
       "2     OCTREOTIDE  1.242924  \n",
       "3  bromocriptine  1.179609  \n",
       "4  bromocriptine  1.155644  "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "#This is the templated query that goes (disease)-(gene)-(disease2), (gene)-(chemical)-[treats]->(disease2)\n",
    "turl=lambda robokop,disease_id,disease_name: f'http://{robokop}/api/simple/quick/template/repurposing_by_gene/{disease_id}/?name1={disease_name}&max_connectivity=1000'\n",
    "\n",
    "for disease_id, disease_name in common_diseases + rare_diseases:\n",
    "    url = turl(robokop,disease_id,disease_name)\n",
    "    display(HTML(f'<h3>{disease_name}</h3>'))\n",
    "    response = requests.get(url)\n",
    "    if response.status_code != 200:\n",
    "        print('Error')\n",
    "        continue\n",
    "    answers=response.json()\n",
    "    view_url = get_view_url(answers)\n",
    "    display(HTML(f'<a href={view_url}>View Answer in ROBOKOP</a>'))\n",
    "    answer_frame = parse_answer(answers,node_list=['n1','n2','n3'],edge_list=[])\n",
    "    display(answer_frame.head())    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
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    "deletable": true,
    "editable": true
   },
   "outputs": [],
   "source": []
  }
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