data_exploration.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 44,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import pickle\n",
    "%matplotlib inline\n",
    "import pandas as pd\n",
    "import seaborn as sns\n",
    "import shelve\n",
    "import re\n",
    "from collections import defaultdict, Counter\n",
    "from tqdm import tqdm\n",
    "import requests\n",
    "from pyquery import PyQuery as pq\n",
    "from collections import OrderedDict"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<pandas.core.config.DictWrapper at 0x7f477bddfa58>"
      ]
     },
     "execution_count": 37,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pd.options.display.width"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 77,
   "metadata": {},
   "outputs": [],
   "source": [
    "pd.set_option(\"display.max_colwidth\", 120)\n",
    "pd.set_option(\"display.width\", 120)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 61,
   "metadata": {},
   "outputs": [],
   "source": [
    "edges = pd.read_csv('edges_biolink.csv')\n",
    "nodes = pd.read_csv(\"nodes_biolink.csv\", index_col=0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 62,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>label</th>\n",
       "      <th>TYPE</th>\n",
       "      <th>bl_type</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ID</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>C0038195</th>\n",
       "      <td>State Medicine</td>\n",
       "      <td>Activities &amp; Behaviors</td>\n",
       "      <td>activity_and_behavior</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>C1290952</th>\n",
       "      <td>Taking medication</td>\n",
       "      <td>Activities &amp; Behaviors</td>\n",
       "      <td>activity_and_behavior</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>C0085092</th>\n",
       "      <td>Parenting behavior</td>\n",
       "      <td>Activities &amp; Behaviors</td>\n",
       "      <td>activity_and_behavior</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>C1096771</th>\n",
       "      <td>Murderer</td>\n",
       "      <td>Activities &amp; Behaviors</td>\n",
       "      <td>activity_and_behavior</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>C1299651</th>\n",
       "      <td>Serious reportable event</td>\n",
       "      <td>Activities &amp; Behaviors</td>\n",
       "      <td>activity_and_behavior</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                             label                    TYPE                bl_type\n",
       "ID                                                                               \n",
       "C0038195            State Medicine  Activities & Behaviors  activity_and_behavior\n",
       "C1290952         Taking medication  Activities & Behaviors  activity_and_behavior\n",
       "C0085092        Parenting behavior  Activities & Behaviors  activity_and_behavior\n",
       "C1096771                  Murderer  Activities & Behaviors  activity_and_behavior\n",
       "C1299651  Serious reportable event  Activities & Behaviors  activity_and_behavior"
      ]
     },
     "execution_count": 62,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "nodes.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 70,
   "metadata": {},
   "outputs": [],
   "source": [
    "node_label = dict(zip(nodes.index, nodes.label))\n",
    "node_type = dict(zip(nodes.index, nodes.bl_type))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 64,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>START_ID</th>\n",
       "      <th>END_ID</th>\n",
       "      <th>pmids</th>\n",
       "      <th>n_pmids</th>\n",
       "      <th>NEG</th>\n",
       "      <th>bl_pred</th>\n",
       "      <th>bl_type</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>C0021769</td>\n",
       "      <td>C1182654</td>\n",
       "      <td>1597294</td>\n",
       "      <td>1</td>\n",
       "      <td>False</td>\n",
       "      <td>ADMINISTERED_TO</td>\n",
       "      <td>chemical_substance.ADMINISTERED_TO.anatomical_entity</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>C0001271</td>\n",
       "      <td>C0007635</td>\n",
       "      <td>6684662;11037792</td>\n",
       "      <td>2</td>\n",
       "      <td>False</td>\n",
       "      <td>ADMINISTERED_TO</td>\n",
       "      <td>chemical_substance.ADMINISTERED_TO.anatomical_entity</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>C0003339</td>\n",
       "      <td>C0014467</td>\n",
       "      <td>11857592</td>\n",
       "      <td>1</td>\n",
       "      <td>False</td>\n",
       "      <td>ADMINISTERED_TO</td>\n",
       "      <td>chemical_substance.ADMINISTERED_TO.anatomical_entity</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>C0028612</td>\n",
       "      <td>C0085080</td>\n",
       "      <td>1985199</td>\n",
       "      <td>1</td>\n",
       "      <td>False</td>\n",
       "      <td>ADMINISTERED_TO</td>\n",
       "      <td>chemical_substance.ADMINISTERED_TO.anatomical_entity</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>C0059249</td>\n",
       "      <td>C0431085</td>\n",
       "      <td>12739069</td>\n",
       "      <td>1</td>\n",
       "      <td>False</td>\n",
       "      <td>ADMINISTERED_TO</td>\n",
       "      <td>chemical_substance.ADMINISTERED_TO.anatomical_entity</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   START_ID    END_ID             pmids  n_pmids    NEG          bl_pred  \\\n",
       "0  C0021769  C1182654           1597294        1  False  ADMINISTERED_TO   \n",
       "1  C0001271  C0007635  6684662;11037792        2  False  ADMINISTERED_TO   \n",
       "2  C0003339  C0014467          11857592        1  False  ADMINISTERED_TO   \n",
       "3  C0028612  C0085080           1985199        1  False  ADMINISTERED_TO   \n",
       "4  C0059249  C0431085          12739069        1  False  ADMINISTERED_TO   \n",
       "\n",
       "                                                bl_type  \n",
       "0  chemical_substance.ADMINISTERED_TO.anatomical_entity  \n",
       "1  chemical_substance.ADMINISTERED_TO.anatomical_entity  \n",
       "2  chemical_substance.ADMINISTERED_TO.anatomical_entity  \n",
       "3  chemical_substance.ADMINISTERED_TO.anatomical_entity  \n",
       "4  chemical_substance.ADMINISTERED_TO.anatomical_entity  "
      ]
     },
     "execution_count": 64,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "edges.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 71,
   "metadata": {},
   "outputs": [],
   "source": [
    "edges['start_label'] = edges.START_ID.map(node_label.get)\n",
    "edges['end_label'] = edges.END_ID.map(node_label.get)\n",
    "edges['start_type'] = edges.START_ID.map(node_type.get)\n",
    "edges['end_type'] = edges.END_ID.map(node_type.get)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 72,
   "metadata": {},
   "outputs": [],
   "source": [
    "edges = edges.sort_values(\"n_pmids\", ascending=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 73,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "    }\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>START_ID</th>\n",
       "      <th>END_ID</th>\n",
       "      <th>pmids</th>\n",
       "      <th>n_pmids</th>\n",
       "      <th>NEG</th>\n",
       "      <th>bl_pred</th>\n",
       "      <th>bl_type</th>\n",
       "      <th>start_label</th>\n",
       "      <th>end_label</th>\n",
       "      <th>start_type</th>\n",
       "      <th>end_type</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>10686996</th>\n",
       "      <td>C0023884</td>\n",
       "      <td>C0034693</td>\n",
       "      <td>6773194;1698569;5076198;20619621;8033224;4155684;6891338;1257600;7974499;20287910;5495281;242406...</td>\n",
       "      <td>45915</td>\n",
       "      <td>False</td>\n",
       "      <td>PART_OF</td>\n",
       "      <td>anatomical_entity.PART_OF.individual_organism</td>\n",
       "      <td>Liver</td>\n",
       "      <td>Rattus norvegicus</td>\n",
       "      <td>anatomical_entity</td>\n",
       "      <td>individual_organism</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10700614</th>\n",
       "      <td>C0006104</td>\n",
       "      <td>C0034693</td>\n",
       "      <td>7142989;1647769;8855842;8836629;21945033;2995978;9252233;11596050;25303736;19785543;16689096;800...</td>\n",
       "      <td>45542</td>\n",
       "      <td>False</td>\n",
       "      <td>PART_OF</td>\n",
       "      <td>anatomical_entity.PART_OF.individual_organism</td>\n",
       "      <td>Brain</td>\n",
       "      <td>Rattus norvegicus</td>\n",
       "      <td>anatomical_entity</td>\n",
       "      <td>individual_organism</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10740905</th>\n",
       "      <td>C0229671</td>\n",
       "      <td>C0030705</td>\n",
       "      <td>3479311;19445843;10895099;3219160;9916062;10219592;21893063;2200820;2515743;8270063;11147755;125...</td>\n",
       "      <td>32877</td>\n",
       "      <td>False</td>\n",
       "      <td>PART_OF</td>\n",
       "      <td>anatomical_entity.PART_OF.individual_organism</td>\n",
       "      <td>Serum</td>\n",
       "      <td>Patients</td>\n",
       "      <td>anatomical_entity</td>\n",
       "      <td>individual_organism</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10741044</th>\n",
       "      <td>C0229671</td>\n",
       "      <td>C0020114</td>\n",
       "      <td>6185150;1413991;9613468;23595366;13326435;19730118;16107258;2266547;26612625;27554022;23305092;4...</td>\n",
       "      <td>25898</td>\n",
       "      <td>False</td>\n",
       "      <td>PART_OF</td>\n",
       "      <td>anatomical_entity.PART_OF.individual_organism</td>\n",
       "      <td>Serum</td>\n",
       "      <td>Human</td>\n",
       "      <td>anatomical_entity</td>\n",
       "      <td>individual_organism</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8819362</th>\n",
       "      <td>C0229671</td>\n",
       "      <td>C0010294</td>\n",
       "      <td>15553306;25813256;21606119;2660616;7694990;18669772;22990506;23541229;9186889;10546024;11805181;...</td>\n",
       "      <td>22475</td>\n",
       "      <td>False</td>\n",
       "      <td>LOCATION_OF</td>\n",
       "      <td>anatomical_entity.LOCATION_OF.chemical_substance</td>\n",
       "      <td>Serum</td>\n",
       "      <td>Creatinine</td>\n",
       "      <td>anatomical_entity</td>\n",
       "      <td>chemical_substance</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "          START_ID    END_ID  \\\n",
       "10686996  C0023884  C0034693   \n",
       "10700614  C0006104  C0034693   \n",
       "10740905  C0229671  C0030705   \n",
       "10741044  C0229671  C0020114   \n",
       "8819362   C0229671  C0010294   \n",
       "\n",
       "                                                                                                        pmids  \\\n",
       "10686996  6773194;1698569;5076198;20619621;8033224;4155684;6891338;1257600;7974499;20287910;5495281;242406...   \n",
       "10700614  7142989;1647769;8855842;8836629;21945033;2995978;9252233;11596050;25303736;19785543;16689096;800...   \n",
       "10740905  3479311;19445843;10895099;3219160;9916062;10219592;21893063;2200820;2515743;8270063;11147755;125...   \n",
       "10741044  6185150;1413991;9613468;23595366;13326435;19730118;16107258;2266547;26612625;27554022;23305092;4...   \n",
       "8819362   15553306;25813256;21606119;2660616;7694990;18669772;22990506;23541229;9186889;10546024;11805181;...   \n",
       "\n",
       "          n_pmids    NEG      bl_pred                                           bl_type  \\\n",
       "10686996    45915  False      PART_OF     anatomical_entity.PART_OF.individual_organism   \n",
       "10700614    45542  False      PART_OF     anatomical_entity.PART_OF.individual_organism   \n",
       "10740905    32877  False      PART_OF     anatomical_entity.PART_OF.individual_organism   \n",
       "10741044    25898  False      PART_OF     anatomical_entity.PART_OF.individual_organism   \n",
       "8819362     22475  False  LOCATION_OF  anatomical_entity.LOCATION_OF.chemical_substance   \n",
       "\n",
       "         start_label          end_label         start_type             end_type  \n",
       "10686996       Liver  Rattus norvegicus  anatomical_entity  individual_organism  \n",
       "10700614       Brain  Rattus norvegicus  anatomical_entity  individual_organism  \n",
       "10740905       Serum           Patients  anatomical_entity  individual_organism  \n",
       "10741044       Serum              Human  anatomical_entity  individual_organism  \n",
       "8819362        Serum         Creatinine  anatomical_entity   chemical_substance  "
      ]
     },
     "execution_count": 73,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "edges.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 79,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "*****chemical_substance*****\n",
      "                          start_label    end_label          start_type             end_type          bl_pred\n",
      "8819362                         Serum   Creatinine   anatomical_entity   chemical_substance      LOCATION_OF\n",
      "8817334                         Serum   Antibodies   anatomical_entity   chemical_substance      LOCATION_OF\n",
      "8522401                        Plasma      Glucose   anatomical_entity   chemical_substance      LOCATION_OF\n",
      "7612743                      Plasmids          DNA  chemical_substance   chemical_substance      SUBCLASS_OF\n",
      "7671835             N-Methylaspartate    Aspartate  chemical_substance   chemical_substance      SUBCLASS_OF\n",
      "11083364                      Calcium   Protoplasm  chemical_substance    anatomical_entity          PART_OF\n",
      "95249     Pharmaceutical Preparations     Patients  chemical_substance  individual_organism  ADMINISTERED_TO\n",
      "8817672                         Serum  Cholesterol   anatomical_entity   chemical_substance      LOCATION_OF\n",
      "8820981                         Serum      Calcium   anatomical_entity   chemical_substance      LOCATION_OF\n",
      "7668851   Tumor Necrosis Factor-alpha     cytokine  chemical_substance   chemical_substance      SUBCLASS_OF\n",
      "\n",
      "*****biological_process*****\n",
      "                     start_label                  end_label          start_type            end_type      bl_pred\n",
      "9779242                 Membrane               Permeability   anatomical_entity  biological_process  LOCATION_OF\n",
      "7920154               experience                   Learning  biological_process  biological_process  SUBCLASS_OF\n",
      "874499                 MicroRNAs            Gene Expression  chemical_substance  biological_process      AFFECTS\n",
      "3423758  Cardiovascular Diseases          Cessation of life             disease  biological_process       CAUSES\n",
      "3421342                  Disease                   Mutation             disease  biological_process       CAUSES\n",
      "7921268                Apoptosis                 Cell Death  biological_process  biological_process  SUBCLASS_OF\n",
      "9784410                    Brain  Potentials, Event-Related   anatomical_entity  biological_process  LOCATION_OF\n",
      "9783415            Cell membrane               Permeability   anatomical_entity  biological_process  LOCATION_OF\n",
      "1452782                    Genes                  Apoptosis      genomic_entity  biological_process      AFFECTS\n",
      "123454                     Cells                  Apoptosis   anatomical_entity  biological_process      AFFECTS\n",
      "\n",
      "*****genomic_entity*****\n",
      "              start_label               end_label         start_type             end_type      bl_pred\n",
      "11671056         CA2 gene              Protoplasm     genomic_entity    anatomical_entity      PART_OF\n",
      "11678998      Genes, rRNA                     16s     genomic_entity    anatomical_entity      PART_OF\n",
      "11670925         CA2 gene           Extracellular     genomic_entity    anatomical_entity      PART_OF\n",
      "9382943             Serum               IGHE gene  anatomical_entity       genomic_entity  LOCATION_OF\n",
      "11883838  Homologous Gene                   Human     genomic_entity  individual_organism      PART_OF\n",
      "7824581          TNF gene                cytokine     genomic_entity   chemical_substance  SUBCLASS_OF\n",
      "11677196        CAMP gene              Protoplasm     genomic_entity    anatomical_entity      PART_OF\n",
      "11673612         CA2 gene                 Cytosol     genomic_entity    anatomical_entity      PART_OF\n",
      "7840404         TP53 gene  Tumor Suppressor Genes     genomic_entity       genomic_entity  SUBCLASS_OF\n",
      "9382280             Serum                LEP gene  anatomical_entity       genomic_entity  LOCATION_OF\n",
      "\n",
      "*****anatomical_entity*****\n",
      "         start_label          end_label         start_type             end_type      bl_pred\n",
      "10686996       Liver  Rattus norvegicus  anatomical_entity  individual_organism      PART_OF\n",
      "10700614       Brain  Rattus norvegicus  anatomical_entity  individual_organism      PART_OF\n",
      "10740905       Serum           Patients  anatomical_entity  individual_organism      PART_OF\n",
      "10741044       Serum              Human  anatomical_entity  individual_organism      PART_OF\n",
      "8819362        Serum         Creatinine  anatomical_entity   chemical_substance  LOCATION_OF\n",
      "10699501       Brain              Human  anatomical_entity  individual_organism      PART_OF\n",
      "8817334        Serum         Antibodies  anatomical_entity   chemical_substance  LOCATION_OF\n",
      "8522401       Plasma            Glucose  anatomical_entity   chemical_substance  LOCATION_OF\n",
      "10528464       Cells             Spleen  anatomical_entity    anatomical_entity      PART_OF\n",
      "10705024         Eye           Patients  anatomical_entity  individual_organism      PART_OF\n",
      "\n",
      "*****activity_and_behavior*****\n",
      "                 start_label    end_label             start_type               end_type      bl_pred\n",
      "7591072              Smoking       Habits  activity_and_behavior  activity_and_behavior  SUBCLASS_OF\n",
      "7590431  Alcohol consumption     Behavior  activity_and_behavior  activity_and_behavior  SUBCLASS_OF\n",
      "7592020             Medicaid     Services  activity_and_behavior  activity_and_behavior  SUBCLASS_OF\n",
      "7590438            Mediating       Events  activity_and_behavior  activity_and_behavior  SUBCLASS_OF\n",
      "7590529           Life Style     Behavior  activity_and_behavior  activity_and_behavior  SUBCLASS_OF\n",
      "7590799             Exercise     Behavior  activity_and_behavior  activity_and_behavior  SUBCLASS_OF\n",
      "7591269              Running  Performance  activity_and_behavior  activity_and_behavior  SUBCLASS_OF\n",
      "7590482           Relaxation     Behavior  activity_and_behavior  activity_and_behavior  SUBCLASS_OF\n",
      "7591331             Swimming     Behavior  activity_and_behavior  activity_and_behavior  SUBCLASS_OF\n",
      "7590511             Gambling     Behavior  activity_and_behavior  activity_and_behavior  SUBCLASS_OF\n",
      "\n",
      "*****individual_organism*****\n",
      "         start_label                 end_label           start_type             end_type      bl_pred\n",
      "10686996       Liver         Rattus norvegicus    anatomical_entity  individual_organism      PART_OF\n",
      "10700614       Brain         Rattus norvegicus    anatomical_entity  individual_organism      PART_OF\n",
      "10740905       Serum                  Patients    anatomical_entity  individual_organism      PART_OF\n",
      "10741044       Serum                     Human    anatomical_entity  individual_organism      PART_OF\n",
      "10699501       Brain                     Human    anatomical_entity  individual_organism      PART_OF\n",
      "10705024         Eye                  Patients    anatomical_entity  individual_organism      PART_OF\n",
      "10685143       Heart         Rattus norvegicus    anatomical_entity  individual_organism      PART_OF\n",
      "7847064      Elderly                   Persons  individual_organism  individual_organism  SUBCLASS_OF\n",
      "10633773  Hepatocyte         Rattus norvegicus    anatomical_entity  individual_organism      PART_OF\n",
      "10647037       Cells  Saccharomyces cerevisiae    anatomical_entity  individual_organism      PART_OF\n",
      "\n",
      "*****named_thing*****\n",
      "                      start_label         end_label   start_type     end_type      bl_pred\n",
      "7916624                  Ceramics         Materials  named_thing  named_thing  SUBCLASS_OF\n",
      "7917457                  Plastics         Materials  named_thing  named_thing  SUBCLASS_OF\n",
      "7916094                  Scaffold         Materials  named_thing  named_thing  SUBCLASS_OF\n",
      "7915897            Nanostructures         Materials  named_thing  named_thing  SUBCLASS_OF\n",
      "7916437  Sodium Chloride, Dietary              Diet  named_thing  named_thing  SUBCLASS_OF\n",
      "7916942                      Food         Materials  named_thing  named_thing  SUBCLASS_OF\n",
      "7917805                      Pork              Meat  named_thing  named_thing  SUBCLASS_OF\n",
      "7917932                Vegetables              Food  named_thing  named_thing  SUBCLASS_OF\n",
      "7915931                 Solutions  Liquid substance  named_thing  named_thing  SUBCLASS_OF\n",
      "7916416                       Tea         Beverages  named_thing  named_thing  SUBCLASS_OF\n",
      "\n",
      "*****disease*****\n",
      "                       start_label            end_label         start_type end_type      bl_pred\n",
      "9330565                      Liver               Injury  anatomical_entity  disease  LOCATION_OF\n",
      "9268225    Head and neck structure  Malignant Neoplasms  anatomical_entity  disease  LOCATION_OF\n",
      "9356522                       Lung               Injury  anatomical_entity  disease  LOCATION_OF\n",
      "7730571  Non-alcoholic fatty liver              Disease            disease  disease  SUBCLASS_OF\n",
      "7754496        Malignant Neoplasms              Disease            disease  disease  SUBCLASS_OF\n",
      "8916557              Blood Vessels               Lesion  anatomical_entity  disease  LOCATION_OF\n",
      "9353826                       Lung               Lesion  anatomical_entity  disease  LOCATION_OF\n",
      "7754043                   Neoplasm               Lesion            disease  disease  SUBCLASS_OF\n",
      "8991914                      Brain               Lesion  anatomical_entity  disease  LOCATION_OF\n",
      "7759907                       Pain             Symptoms            disease  disease  SUBCLASS_OF\n"
     ]
    }
   ],
   "source": [
    "cols = ['start_label', 'end_label', 'start_type', 'end_type', 'bl_pred']\n",
    "for node_type in set(nodes.bl_type):\n",
    "    print(\"\\n*****{}*****\".format(node_type))\n",
    "    print(edges[(edges.start_type == node_type) | (edges.end_type == node_type)][cols].head(10))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 55,
   "metadata": {},
   "outputs": [],
   "source": [
    "types = set(edges.bl_pred)\n",
    "t = list(types)[0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 58,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "*****COEXISTS_WITH*****\n",
      "\n",
      "top 5 edges\n",
      "         START_ID    END_ID                                          bl_type  \\\n",
      "5107643  C0752046  C0017337      genomic_entity.COEXISTS_WITH.genomic_entity   \n",
      "4221706  C0012854  C0162326  chemical_substance.COEXISTS_WITH.genomic_entity   \n",
      "4747477  C0021368  C0004096                    disease.COEXISTS_WITH.disease   \n",
      "4845109  C0338656  C0002395                    disease.COEXISTS_WITH.disease   \n",
      "4504882  C0277785  C0036341                    disease.COEXISTS_WITH.disease   \n",
      "\n",
      "                            start_label            end_label  \n",
      "5107643  Single Nucleotide Polymorphism                Genes  \n",
      "4221706                             DNA         DNA Sequence  \n",
      "4747477                    Inflammation               Asthma  \n",
      "4845109              Impaired cognition  Alzheimer's Disease  \n",
      "4504882             Functional disorder        Schizophrenia  \n",
      "\n",
      "top 5 start\n",
      "['Single Nucleotide Polymorphism', 'DNA', 'Inflammation', 'Impaired cognition', 'Functional disorder']\n",
      "\n",
      "top 5 end\n",
      "['Genes', 'DNA Sequence', 'Asthma', \"Alzheimer's Disease\", 'Schizophrenia']\n",
      "\n",
      "*****NEGATIVELY_REGULATES*****\n",
      "\n",
      "top 5 edges\n",
      "         START_ID    END_ID                                                     bl_type  \\\n",
      "5919369  C0012544  C0005974  chemical_substance.NEGATIVELY_REGULATES.biological_process   \n",
      "5915173  C0534628  C0302600  chemical_substance.NEGATIVELY_REGULATES.biological_process   \n",
      "5925108  C0028978  C0232552  chemical_substance.NEGATIVELY_REGULATES.biological_process   \n",
      "5920507  C0006668  C0005974  chemical_substance.NEGATIVELY_REGULATES.biological_process   \n",
      "5925190  C1142985  C0021826  chemical_substance.NEGATIVELY_REGULATES.biological_process   \n",
      "\n",
      "            start_label               end_label  \n",
      "5919369  Diphosphonates         Bone Resorption  \n",
      "5915173     Endostatins            Angiogenesis  \n",
      "5925108      Omeprazole  Gastric acid secretion  \n",
      "5920507      Calcitonin         Bone Resorption  \n",
      "5925190       ezetimibe   Intestinal Absorption  \n",
      "\n",
      "top 5 start\n",
      "['Diphosphonates', 'Endostatins', 'Omeprazole', 'Calcitonin', 'ezetimibe']\n",
      "\n",
      "top 5 end\n",
      "['Bone Resorption', 'Angiogenesis', 'Gastric acid secretion', 'Intestinal Absorption', 'glucose output']\n",
      "\n",
      "*****ADMINISTERED_TO*****\n",
      "\n",
      "top 5 edges\n",
      "       START_ID    END_ID                                                 bl_type  \\\n",
      "95249  C0013227  C0030705  chemical_substance.ADMINISTERED_TO.individual_organism   \n",
      "36017  C0003232  C0030705  chemical_substance.ADMINISTERED_TO.individual_organism   \n",
      "2850   C0032136  C0007634    chemical_substance.ADMINISTERED_TO.anatomical_entity   \n",
      "53706  C0037494  C0034693  chemical_substance.ADMINISTERED_TO.individual_organism   \n",
      "76631  C0004057  C0030705  chemical_substance.ADMINISTERED_TO.individual_organism   \n",
      "\n",
      "                       start_label          end_label  \n",
      "95249  Pharmaceutical Preparations           Patients  \n",
      "36017                  Antibiotics           Patients  \n",
      "2850                      Plasmids              Cells  \n",
      "53706              Sodium Chloride  Rattus norvegicus  \n",
      "76631                      Aspirin           Patients  \n",
      "\n",
      "top 5 start\n",
      "['Pharmaceutical Preparations', 'Antibiotics', 'Plasmids', 'Sodium Chloride', 'Aspirin']\n",
      "\n",
      "top 5 end\n",
      "['Patients', 'Cells', 'Rattus norvegicus', 'Woman', 'Control Groups']\n",
      "\n",
      "*****CONVERTS_TO*****\n",
      "\n",
      "top 5 edges\n",
      "         START_ID    END_ID                                            bl_type  \\\n",
      "5276183  C1417760  C0028128      genomic_entity.CONVERTS_TO.chemical_substance   \n",
      "5244863  C0669372  C0028128  chemical_substance.CONVERTS_TO.chemical_substance   \n",
      "5259244  C0003320  C0030956  chemical_substance.CONVERTS_TO.chemical_substance   \n",
      "5275113  C1328053  C0028128      genomic_entity.CONVERTS_TO.chemical_substance   \n",
      "5268896  C0085151  C1364818      chemical_substance.CONVERTS_TO.genomic_entity   \n",
      "\n",
      "                            start_label     end_label  \n",
      "5276183                       NOS2 gene  Nitric Oxide  \n",
      "5244863            NOS2A protein, human  Nitric Oxide  \n",
      "5259244                        Antigens      Peptides  \n",
      "5275113                       NOS3 gene  Nitric Oxide  \n",
      "5268896  Amyloid beta-Protein Precursor      APP gene  \n",
      "\n",
      "top 5 start\n",
      "['NOS2 gene', 'NOS2A protein, human', 'Antigens', 'NOS3 gene', 'Amyloid beta-Protein Precursor']\n",
      "\n",
      "top 5 end\n",
      "['Nitric Oxide', 'Peptides', 'APP gene', 'Lactate', 'Prostaglandins']\n",
      "\n",
      "*****RELATED_TO*****\n",
      "\n",
      "top 5 edges\n",
      "         START_ID    END_ID                                bl_type start_label  \\\n",
      "2013085  C1101610  C0006826  chemical_substance.RELATED_TO.disease   MicroRNAs   \n",
      "1828994  C0079189  C0699748  chemical_substance.RELATED_TO.disease    cytokine   \n",
      "2084208  C1457887  C0012634             disease.RELATED_TO.disease    Symptoms   \n",
      "2048556  C0299583  C0028754  chemical_substance.RELATED_TO.disease      Leptin   \n",
      "1968646  C0002716  C0002395  chemical_substance.RELATED_TO.disease     Amyloid   \n",
      "\n",
      "                   end_label  \n",
      "2013085  Malignant Neoplasms  \n",
      "1828994         Pathogenesis  \n",
      "2084208              Disease  \n",
      "2048556              Obesity  \n",
      "1968646  Alzheimer's Disease  \n",
      "\n",
      "top 5 start\n",
      "['MicroRNAs', 'cytokine', 'Symptoms', 'Leptin', 'Amyloid']\n",
      "\n",
      "top 5 end\n",
      "['Malignant Neoplasms', 'Pathogenesis', 'Disease', 'Obesity', \"Alzheimer's Disease\"]\n",
      "\n",
      "*****PREVENTS*****\n",
      "\n",
      "top 5 edges\n",
      "          START_ID    END_ID                                 bl_type                  start_label  \\\n",
      "12197694  C1273870  C0009566  activity_and_behavior.PREVENTS.disease         Management procedure   \n",
      "12267167  C0042210  C0012634     chemical_substance.PREVENTS.disease                     Vaccines   \n",
      "12208790  C0013227  C0879626     chemical_substance.PREVENTS.disease  Pharmaceutical Preparations   \n",
      "12267854  C0003402  C0242606     chemical_substance.PREVENTS.disease                 Antioxidants   \n",
      "12211852  C0043031  C0038454     chemical_substance.PREVENTS.disease                     Warfarin   \n",
      "\n",
      "                         end_label  \n",
      "12197694              Complication  \n",
      "12267167                   Disease  \n",
      "12208790           Adverse effects  \n",
      "12267854          Oxidative Stress  \n",
      "12211852  Cerebrovascular accident  \n",
      "\n",
      "top 5 start\n",
      "['Management procedure', 'Vaccines', 'Pharmaceutical Preparations', 'Antioxidants', 'Warfarin']\n",
      "\n",
      "top 5 end\n",
      "['Complication', 'Disease', 'Adverse effects', 'Oxidative Stress', 'Cerebrovascular accident']\n",
      "\n",
      "*****STIMULATES*****\n",
      "\n",
      "top 5 edges\n",
      "          START_ID    END_ID                                           bl_type  \\\n",
      "12741497  C0016601  C0001492  chemical_substance.STIMULATES.chemical_substance   \n",
      "13171816  C0039654  C0033634  chemical_substance.STIMULATES.chemical_substance   \n",
      "13468194  C1422569  C0039654      genomic_entity.STIMULATES.chemical_substance   \n",
      "12806553  C0023810  C1456820  chemical_substance.STIMULATES.chemical_substance   \n",
      "13322964  C0812246  C0023810      genomic_entity.STIMULATES.chemical_substance   \n",
      "\n",
      "                           start_label                     end_label  \n",
      "12741497                     Forskolin             Adenylate Cyclase  \n",
      "13171816  Tetradecanoylphorbol Acetate              Protein Kinase C  \n",
      "13468194                   SPANXC gene  Tetradecanoylphorbol Acetate  \n",
      "12806553           Lipopolysaccharides   Tumor Necrosis Factor-alpha  \n",
      "13322964                      TNF gene           Lipopolysaccharides  \n",
      "\n",
      "top 5 start\n",
      "['Forskolin', 'Tetradecanoylphorbol Acetate', 'SPANXC gene', 'Lipopolysaccharides', 'TNF gene']\n",
      "\n",
      "top 5 end\n",
      "['Adenylate Cyclase', 'Protein Kinase C', 'Tetradecanoylphorbol Acetate', 'Tumor Necrosis Factor-alpha', 'Lipopolysaccharides']\n",
      "\n",
      "*****TREATS*****\n",
      "\n",
      "top 5 edges\n",
      "          START_ID    END_ID                            bl_type                  start_label  \\\n",
      "13929024  C0013227  C0012634  chemical_substance.TREATS.disease  Pharmaceutical Preparations   \n",
      "13937544  C0013227  C0020538  chemical_substance.TREATS.disease  Pharmaceutical Preparations   \n",
      "14150488  C0039286  C0006142  chemical_substance.TREATS.disease                    Tamoxifen   \n",
      "14037429  C0040615  C0036341  chemical_substance.TREATS.disease         Antipsychotic Agents   \n",
      "13927916  C0013227  C0006826  chemical_substance.TREATS.disease  Pharmaceutical Preparations   \n",
      "\n",
      "                             end_label  \n",
      "13929024                       Disease  \n",
      "13937544          Hypertensive disease  \n",
      "14150488  Malignant neoplasm of breast  \n",
      "14037429                 Schizophrenia  \n",
      "13927916           Malignant Neoplasms  \n",
      "\n",
      "top 5 start\n",
      "['Pharmaceutical Preparations', 'Tamoxifen', 'Antipsychotic Agents', 'Antibiotics', 'Methotrexate']\n",
      "\n",
      "top 5 end\n",
      "['Disease', 'Hypertensive disease', 'Malignant neoplasm of breast', 'Schizophrenia', 'Malignant Neoplasms']\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "*****INTERACTS_WITH*****\n",
      "\n",
      "top 5 edges\n",
      "         START_ID    END_ID                                               bl_type  \\\n",
      "7361227  C1366628  C0596902      genomic_entity.INTERACTS_WITH.chemical_substance   \n",
      "7136191  C0017337  C0040648      genomic_entity.INTERACTS_WITH.chemical_substance   \n",
      "7379769  C1366832  C0596902      genomic_entity.INTERACTS_WITH.chemical_substance   \n",
      "6943786  C0003241  C0003320  chemical_substance.INTERACTS_WITH.chemical_substance   \n",
      "6457818  C0033684  C0012854  chemical_substance.INTERACTS_WITH.chemical_substance   \n",
      "\n",
      "                                                                    start_label  \\\n",
      "7361227                                                             ATP8A2 gene   \n",
      "7136191                                                                   Genes   \n",
      "7379769  ATPase, Aminophospholipid Transporter-Like, Class I, Type 8A, Member 2   \n",
      "6943786                                                              Antibodies   \n",
      "6457818                                                                Proteins   \n",
      "\n",
      "                           end_label  \n",
      "7361227  Membrane Transport Proteins  \n",
      "7136191         TRANSCRIPTION FACTOR  \n",
      "7379769  Membrane Transport Proteins  \n",
      "6943786                     Antigens  \n",
      "6457818                          DNA  \n",
      "\n",
      "top 5 start\n",
      "['ATP8A2 gene', 'Genes', 'ATPase, Aminophospholipid Transporter-Like, Class I, Type 8A, Member 2', 'Antibodies', 'Proteins']\n",
      "\n",
      "top 5 end\n",
      "['Membrane Transport Proteins', 'TRANSCRIPTION FACTOR', 'Antigens', 'DNA', 'TP53 gene']\n",
      "\n",
      "*****MANIFESTATION_OF*****\n",
      "\n",
      "top 5 edges\n",
      "         START_ID    END_ID                           bl_type         start_label  \\\n",
      "9811276  C0497327  C0002395  disease.MANIFESTATION_OF.disease            Dementia   \n",
      "9815062  C0009566  C0175677  disease.MANIFESTATION_OF.disease        Complication   \n",
      "9810431  C0025362  C0016667  disease.MANIFESTATION_OF.disease  Mental Retardation   \n",
      "9800878  C0012634  C0699748  disease.MANIFESTATION_OF.disease             Disease   \n",
      "9813471  C0231170  C0011581  disease.MANIFESTATION_OF.disease      Disability NOS   \n",
      "\n",
      "                   end_label  \n",
      "9811276  Alzheimer's Disease  \n",
      "9815062               Injury  \n",
      "9810431   Fragile X Syndrome  \n",
      "9800878         Pathogenesis  \n",
      "9813471  Depressive disorder  \n",
      "\n",
      "top 5 start\n",
      "['Dementia', 'Complication', 'Mental Retardation', 'Disease', 'Disability NOS']\n",
      "\n",
      "top 5 end\n",
      "[\"Alzheimer's Disease\", 'Injury', 'Fragile X Syndrome', 'Pathogenesis', 'Depressive disorder']\n",
      "\n",
      "*****NEGATIVELY_REGULATES_ENTITY_TO_ENTITY*****\n",
      "\n",
      "top 5 edges\n",
      "         START_ID    END_ID  \\\n",
      "5972257  C0079419  C0079419   \n",
      "5791597  C0297666  C0812252   \n",
      "5825836  C0251991  C0812228   \n",
      "5790733  C0297666  C1366876   \n",
      "5870660  C0075193  C1422569   \n",
      "\n",
      "                                                                         bl_type    start_label  \\\n",
      "5972257      genomic_entity.NEGATIVELY_REGULATES_ENTITY_TO_ENTITY.genomic_entity      TP53 gene   \n",
      "5791597  chemical_substance.NEGATIVELY_REGULATES_ENTITY_TO_ENTITY.genomic_entity      SB 203580   \n",
      "5825836  chemical_substance.NEGATIVELY_REGULATES_ENTITY_TO_ENTITY.genomic_entity      LY 294002   \n",
      "5790733  chemical_substance.NEGATIVELY_REGULATES_ENTITY_TO_ENTITY.genomic_entity      SB 203580   \n",
      "5870660  chemical_substance.NEGATIVELY_REGULATES_ENTITY_TO_ENTITY.genomic_entity  Staurosporine   \n",
      "\n",
      "           end_label  \n",
      "5972257    TP53 gene  \n",
      "5791597     CRK gene  \n",
      "5825836    AKT1 gene  \n",
      "5790733  MAPK14 gene  \n",
      "5870660  SPANXC gene  \n",
      "\n",
      "top 5 start\n",
      "['TP53 gene', 'SB 203580', 'LY 294002', 'Staurosporine', 'Nitric Oxide']\n",
      "\n",
      "top 5 end\n",
      "['TP53 gene', 'CRK gene', 'AKT1 gene', 'MAPK14 gene', 'SPANXC gene']\n",
      "\n",
      "*****GENE_ASSOCIATED_WITH_CONDITION*****\n",
      "\n",
      "top 5 edges\n",
      "         START_ID    END_ID                                                bl_type  \\\n",
      "2185870  C0079419  C0006826  genomic_entity.GENE_ASSOCIATED_WITH_CONDITION.disease   \n",
      "2225145  C0079427  C0006826  genomic_entity.GENE_ASSOCIATED_WITH_CONDITION.disease   \n",
      "2179951  C0079419  C0027651  genomic_entity.GENE_ASSOCIATED_WITH_CONDITION.disease   \n",
      "2348378  C0017337  C0012634  genomic_entity.GENE_ASSOCIATED_WITH_CONDITION.disease   \n",
      "2347373  C0017337  C0006826  genomic_entity.GENE_ASSOCIATED_WITH_CONDITION.disease   \n",
      "\n",
      "                    start_label            end_label  \n",
      "2185870               TP53 gene  Malignant Neoplasms  \n",
      "2225145  Tumor Suppressor Genes  Malignant Neoplasms  \n",
      "2179951               TP53 gene             Neoplasm  \n",
      "2348378                   Genes              Disease  \n",
      "2347373                   Genes  Malignant Neoplasms  \n",
      "\n",
      "top 5 start\n",
      "['TP53 gene', 'Tumor Suppressor Genes', 'Genes', 'APP gene', 'EGFR gene']\n",
      "\n",
      "top 5 end\n",
      "['Malignant Neoplasms', 'Neoplasm', 'Disease', \"Alzheimer's Disease\", 'Carcinoma, Non-Small-Cell Lung']\n",
      "\n",
      "*****PRODUCES*****\n",
      "\n",
      "top 5 edges\n",
      "          START_ID    END_ID                                        bl_type   start_label  \\\n",
      "12314391  C0007634  C0079189  anatomical_entity.PRODUCES.chemical_substance         Cells   \n",
      "12363529  C0039194  C0079189  anatomical_entity.PRODUCES.chemical_substance  T-Lymphocyte   \n",
      "12361692  C0039194  C0021740  anatomical_entity.PRODUCES.chemical_substance  T-Lymphocyte   \n",
      "12374489  C0020204  C0003250  anatomical_entity.PRODUCES.chemical_substance    Hybridomas   \n",
      "12611015  C1417760  C0028128     genomic_entity.PRODUCES.chemical_substance     NOS2 gene   \n",
      "\n",
      "                             end_label  \n",
      "12314391                      cytokine  \n",
      "12363529                      cytokine  \n",
      "12361692  Recombinant Interferon-gamma  \n",
      "12374489         Monoclonal Antibodies  \n",
      "12611015                  Nitric Oxide  \n",
      "\n",
      "top 5 start\n",
      "['Cells', 'T-Lymphocyte', 'Hybridomas', 'NOS2 gene', 'NOS2A protein, human']\n",
      "\n",
      "top 5 end\n",
      "['cytokine', 'Recombinant Interferon-gamma', 'Monoclonal Antibodies', 'Nitric Oxide', 'IL2 gene']\n",
      "\n",
      "*****CAUSES*****\n",
      "\n",
      "top 5 edges\n",
      "         START_ID    END_ID                            bl_type               start_label  \\\n",
      "3423758  C0007222  C0011065  disease.CAUSES.biological_process   Cardiovascular Diseases   \n",
      "3421342  C0012634  C0026882  disease.CAUSES.biological_process                   Disease   \n",
      "3439588  C0038454  C0011065  disease.CAUSES.biological_process  Cerebrovascular accident   \n",
      "3003376  C0038432  C0011847  chemical_substance.CAUSES.disease              Streptozocin   \n",
      "3431401  C0012634  C0011065  disease.CAUSES.biological_process                   Disease   \n",
      "\n",
      "                 end_label  \n",
      "3423758  Cessation of life  \n",
      "3421342           Mutation  \n",
      "3439588  Cessation of life  \n",
      "3003376           Diabetes  \n",
      "3431401  Cessation of life  \n",
      "\n",
      "top 5 start\n",
      "['Cardiovascular Diseases', 'Disease', 'Cerebrovascular accident', 'Streptozocin', 'TP53 gene']\n",
      "\n",
      "top 5 end\n",
      "['Cessation of life', 'Mutation', 'Diabetes', 'Apoptosis', 'Lack of sensation']\n",
      "\n",
      "*****AFFECTS*****\n",
      "\n",
      "top 5 edges\n",
      "         START_ID    END_ID                                        bl_type start_label  \\\n",
      "874499   C1101610  C0017262  chemical_substance.AFFECTS.biological_process   MicroRNAs   \n",
      "1100759  C0012634  C0030705            disease.AFFECTS.individual_organism     Disease   \n",
      "1026185  C0012634  C0699748                        disease.AFFECTS.disease     Disease   \n",
      "1452782  C0017337  C0162638      genomic_entity.AFFECTS.biological_process       Genes   \n",
      "123454   C0007634  C0162638   anatomical_entity.AFFECTS.biological_process       Cells   \n",
      "\n",
      "               end_label  \n",
      "874499   Gene Expression  \n",
      "1100759         Patients  \n",
      "1026185     Pathogenesis  \n",
      "1452782        Apoptosis  \n",
      "123454         Apoptosis  \n",
      "\n",
      "top 5 start\n",
      "['MicroRNAs', 'Disease', 'Genes', 'Cells', 'Proteins']\n",
      "\n",
      "top 5 end\n",
      "['Gene Expression', 'Patients', 'Pathogenesis', 'Apoptosis', 'Transcription, Genetic']\n",
      "\n",
      "*****PRECEDES*****\n",
      "\n",
      "top 5 edges\n",
      "          START_ID    END_ID                                         bl_type  \\\n",
      "11970524  C0005615  C0032961  biological_process.PRECEDES.biological_process   \n",
      "11956822  C0038525  C0265110                        disease.PRECEDES.disease   \n",
      "11956856  C0038525  C0085616                        disease.PRECEDES.disease   \n",
      "11950313  C0027051  C0018801                        disease.PRECEDES.disease   \n",
      "11974090  C0005615  C0018270  biological_process.PRECEDES.biological_process   \n",
      "\n",
      "                      start_label           end_label  \n",
      "11970524                    Birth           Pregnancy  \n",
      "11956822  Subarachnoid Hemorrhage  Cerebral Vasospasm  \n",
      "11956856  Subarachnoid Hemorrhage           Vasospasm  \n",
      "11950313    Myocardial Infarction       Heart failure  \n",
      "11974090                    Birth              Growth  \n",
      "\n",
      "top 5 start\n",
      "['Birth', 'Subarachnoid Hemorrhage', 'Myocardial Infarction', 'Cerebrovascular accident', 'Injury']\n",
      "\n",
      "top 5 end\n",
      "['Pregnancy', 'Cerebral Vasospasm', 'Vasospasm', 'Heart failure', 'Growth']\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "*****PREDISPOSES*****\n",
      "\n",
      "top 5 edges\n",
      "          START_ID    END_ID                                 bl_type           start_label  \\\n",
      "12019110  C0006560  C0021368  chemical_substance.PREDISPOSES.disease    C-reactive protein   \n",
      "12074270  C0020538  C0007222             disease.PREDISPOSES.disease  Hypertensive disease   \n",
      "12105977  C0948265  C0007222             disease.PREDISPOSES.disease    Metabolic syndrome   \n",
      "12077203  C0004238  C0038454             disease.PREDISPOSES.disease   Atrial Fibrillation   \n",
      "12069465  C0028754  C0007222             disease.PREDISPOSES.disease               Obesity   \n",
      "\n",
      "                         end_label  \n",
      "12019110              Inflammation  \n",
      "12074270   Cardiovascular Diseases  \n",
      "12105977   Cardiovascular Diseases  \n",
      "12077203  Cerebrovascular accident  \n",
      "12069465   Cardiovascular Diseases  \n",
      "\n",
      "top 5 start\n",
      "['C-reactive protein', 'Hypertensive disease', 'Metabolic syndrome', 'Atrial Fibrillation', 'Obesity']\n",
      "\n",
      "top 5 end\n",
      "['Inflammation', 'Cardiovascular Diseases', 'Cerebrovascular accident', 'Diabetes Mellitus, Non-Insulin-Dependent', \"Alzheimer's Disease\"]\n",
      "\n",
      "*****PART_OF*****\n",
      "\n",
      "top 5 edges\n",
      "          START_ID    END_ID                                        bl_type start_label  \\\n",
      "10686996  C0023884  C0034693  anatomical_entity.PART_OF.individual_organism       Liver   \n",
      "10700614  C0006104  C0034693  anatomical_entity.PART_OF.individual_organism       Brain   \n",
      "10740905  C0229671  C0030705  anatomical_entity.PART_OF.individual_organism       Serum   \n",
      "10741044  C0229671  C0020114  anatomical_entity.PART_OF.individual_organism       Serum   \n",
      "10699501  C0006104  C0020114  anatomical_entity.PART_OF.individual_organism       Brain   \n",
      "\n",
      "                  end_label  \n",
      "10686996  Rattus norvegicus  \n",
      "10700614  Rattus norvegicus  \n",
      "10740905           Patients  \n",
      "10741044              Human  \n",
      "10699501              Human  \n",
      "\n",
      "top 5 start\n",
      "['Liver', 'Brain', 'Serum', 'Cells', 'Eye']\n",
      "\n",
      "top 5 end\n",
      "['Rattus norvegicus', 'Patients', 'Human', 'Spleen', 'Blood Vessels']\n",
      "\n",
      "*****SUBCLASS_OF*****\n",
      "\n",
      "top 5 edges\n",
      "         START_ID    END_ID                                                  bl_type  \\\n",
      "7847064  C0001792  C0027361      individual_organism.SUBCLASS_OF.individual_organism   \n",
      "7612743  C0032136  C0012854        chemical_substance.SUBCLASS_OF.chemical_substance   \n",
      "7671835  C0079883  C0085845        chemical_substance.SUBCLASS_OF.chemical_substance   \n",
      "7730571  C0400966  C0012634                              disease.SUBCLASS_OF.disease   \n",
      "7591072  C0037369  C0018464  activity_and_behavior.SUBCLASS_OF.activity_and_behavior   \n",
      "\n",
      "                       start_label  end_label  \n",
      "7847064                    Elderly    Persons  \n",
      "7612743                   Plasmids        DNA  \n",
      "7671835          N-Methylaspartate  Aspartate  \n",
      "7730571  Non-alcoholic fatty liver    Disease  \n",
      "7591072                    Smoking     Habits  \n",
      "\n",
      "top 5 start\n",
      "['Elderly', 'Plasmids', 'N-Methylaspartate', 'Non-alcoholic fatty liver', 'Smoking']\n",
      "\n",
      "top 5 end\n",
      "['Persons', 'DNA', 'Aspartate', 'Disease', 'Habits']\n",
      "\n",
      "*****AUGMENTS*****\n",
      "\n",
      "top 5 edges\n",
      "         START_ID    END_ID                                         bl_type          start_label  \\\n",
      "2838819  C1823619  C0302600      genomic_entity.AUGMENTS.biological_process           VEGFA gene   \n",
      "2725008  C0042210  C0301872  chemical_substance.AUGMENTS.biological_process             Vaccines   \n",
      "2656392  C0021641  C0031715  chemical_substance.AUGMENTS.biological_process              Insulin   \n",
      "2654481  C0021641  C0599781  chemical_substance.AUGMENTS.biological_process              Insulin   \n",
      "2720519  C1171892  C0302600  chemical_substance.AUGMENTS.biological_process  VEGF protein, human   \n",
      "\n",
      "               end_label  \n",
      "2838819     Angiogenesis  \n",
      "2725008  Immune response  \n",
      "2656392  Phosphorylation  \n",
      "2654481   glucose uptake  \n",
      "2720519     Angiogenesis  \n",
      "\n",
      "top 5 start\n",
      "['VEGFA gene', 'Vaccines', 'Insulin', 'VEGF protein, human', 'Glucose']\n",
      "\n",
      "top 5 end\n",
      "['Angiogenesis', 'Immune response', 'Phosphorylation', 'glucose uptake', 'insulin secretion']\n",
      "\n",
      "*****POSITIVELY_REGULATES_ENTITY_TO_ENTITY*****\n",
      "\n",
      "top 5 edges\n",
      "          START_ID    END_ID                                                              bl_type  \\\n",
      "13694076  C0079419  C0079419  genomic_entity.POSITIVELY_REGULATES_ENTITY_TO_ENTITY.genomic_entity   \n",
      "13692963  C0079419  C0249197  genomic_entity.POSITIVELY_REGULATES_ENTITY_TO_ENTITY.genomic_entity   \n",
      "13618112  C0812228  C0812228  genomic_entity.POSITIVELY_REGULATES_ENTITY_TO_ENTITY.genomic_entity   \n",
      "13689970  C1422569  C1422569  genomic_entity.POSITIVELY_REGULATES_ENTITY_TO_ENTITY.genomic_entity   \n",
      "13699356  C1367721  C1367721  genomic_entity.POSITIVELY_REGULATES_ENTITY_TO_ENTITY.genomic_entity   \n",
      "\n",
      "          start_label    end_label  \n",
      "13694076    TP53 gene    TP53 gene  \n",
      "13692963    TP53 gene  CDKN1A gene  \n",
      "13618112    AKT1 gene    AKT1 gene  \n",
      "13689970  SPANXC gene  SPANXC gene  \n",
      "13699356     EGF gene     EGF gene  \n",
      "\n",
      "top 5 start\n",
      "['TP53 gene', 'AKT1 gene', 'SPANXC gene', 'EGF gene', 'TNF gene']\n",
      "\n",
      "top 5 end\n",
      "['TP53 gene', 'CDKN1A gene', 'AKT1 gene', 'SPANXC gene', 'EGF gene']\n",
      "\n",
      "*****LOCATION_OF*****\n",
      "\n",
      "top 5 edges\n",
      "         START_ID    END_ID                                           bl_type  \\\n",
      "8819362  C0229671  C0010294  anatomical_entity.LOCATION_OF.chemical_substance   \n",
      "8817334  C0229671  C0003241  anatomical_entity.LOCATION_OF.chemical_substance   \n",
      "8522401  C0032105  C0017725  anatomical_entity.LOCATION_OF.chemical_substance   \n",
      "9330565  C0023884  C0175677             anatomical_entity.LOCATION_OF.disease   \n",
      "9268225  C0460004  C0006826             anatomical_entity.LOCATION_OF.disease   \n",
      "\n",
      "                     start_label            end_label  \n",
      "8819362                    Serum           Creatinine  \n",
      "8817334                    Serum           Antibodies  \n",
      "8522401                   Plasma              Glucose  \n",
      "9330565                    Liver               Injury  \n",
      "9268225  Head and neck structure  Malignant Neoplasms  \n",
      "\n",
      "top 5 start\n",
      "['Serum', 'Plasma', 'Liver', 'Head and neck structure', 'Lung']\n",
      "\n",
      "top 5 end\n",
      "['Creatinine', 'Antibodies', 'Glucose', 'Injury', 'Malignant Neoplasms']\n",
      "\n",
      "*****COMPLICATES*****\n",
      "\n",
      "top 5 edges\n",
      "         START_ID    END_ID                      bl_type               start_label  \\\n",
      "5202734  C0036980  C0155626  disease.COMPLICATES.disease        Shock, Cardiogenic   \n",
      "5203588  C0036980  C0027051  disease.COMPLICATES.disease        Shock, Cardiogenic   \n",
      "5208974  C0018801  C0155626  disease.COMPLICATES.disease             Heart failure   \n",
      "5199880  C0042510  C0155626  disease.COMPLICATES.disease  Ventricular Fibrillation   \n",
      "5213211  C0019080  C0030920  disease.COMPLICATES.disease                Hemorrhage   \n",
      "\n",
      "                           end_label  \n",
      "5202734  Acute myocardial infarction  \n",
      "5203588        Myocardial Infarction  \n",
      "5208974  Acute myocardial infarction  \n",
      "5199880  Acute myocardial infarction  \n",
      "5213211                 Peptic Ulcer  \n",
      "\n",
      "top 5 start\n",
      "['Shock, Cardiogenic', 'Heart failure', 'Ventricular Fibrillation', 'Hemorrhage', 'Vitreoretinopathy, Proliferative']\n",
      "\n",
      "top 5 end\n",
      "['Acute myocardial infarction', 'Myocardial Infarction', 'Peptic Ulcer', 'Retinal Detachment', 'Pre-Eclampsia']\n"
     ]
    }
   ],
   "source": [
    "for t in types:\n",
    "    s = edges[edges.bl_pred == t].sort_values(\"n_pmids\", ascending=False)[['START_ID', 'END_ID', 'bl_type', 'start_label', 'end_label']]\n",
    "    print(\"\\n*****{}*****\".format(t))\n",
    "    print(\"\\ntop 5 edges\")\n",
    "    print(s.head())\n",
    "    print(\"\\ntop 5 start\")\n",
    "    print(list(OrderedDict.fromkeys(s.start_label))[:5])\n",
    "    print(\"\\ntop 5 end\")\n",
    "    print(list(OrderedDict.fromkeys(s.end_label))[:5])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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