notebooks/api-demo.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# MELODI Presto API Example Usage"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import json\n",
    "import pandas as pd\n",
    "import requests"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Configure parameters"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "API_URL = \"https://melodi-presto.mrcieu.ac.uk/api/\"\n",
    "\n",
    "requests.get(f\"{API_URL}/status\").json()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Create functions for the endpoints\n",
    "\n",
    "Each of the endoints can be wrapped up in a function:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "#enrich\n",
    "def enrich(q):\n",
    "    endpoint = \"/enrich/\"\n",
    "    url = f\"{API_URL}{endpoint}\"\n",
    "    params = {\n",
    "        \"query\": q,\n",
    "    }\n",
    "    response = requests.post(url, data=json.dumps(params))\n",
    "    try:\n",
    "        res = response.json()\n",
    "        enrich_df = (\n",
    "                pd.json_normalize(res)\n",
    "        )\n",
    "        return enrich_df\n",
    "    except:\n",
    "        print('No data')\n",
    "        return []\n",
    "    \n",
    "#overlap\n",
    "def overlap(q1,q2):\n",
    "    endpoint = \"/overlap/\"\n",
    "    url = f\"{API_URL}{endpoint}\"\n",
    "    params = {\n",
    "        \"x\": q1,\n",
    "        \"y\": q2,\n",
    "    }\n",
    "    response = requests.post(url, data=json.dumps(params))\n",
    "    res = response.json()\n",
    "    if 'data' in res:\n",
    "        overlap_df = (    \n",
    "            pd.json_normalize(res['data'])\n",
    "        )\n",
    "    else:\n",
    "        overlap_df=pd.DataFrame()\n",
    "    return overlap_df\n",
    "\n",
    "def sentence(q):\n",
    "    endpoint = \"/sentence/\"\n",
    "    url = f\"{API_URL}{endpoint}\"\n",
    "    params = {\n",
    "        \"pmid\": pmid,\n",
    "    }\n",
    "    response = requests.post(url, data=json.dumps(params))\n",
    "    res = response.json()\n",
    "    pub_df = (\n",
    "        pd.json_normalize(res['data'])\n",
    "    )\n",
    "    return pub_df"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Some extra functions\n",
    "\n",
    "It may also be useful to filter the overlap records to exclude any results derived from the same publication"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "def pub_check(row):\n",
    "    px = set(row['pmids_x'].split(' '))\n",
    "    py = set(row['pmids_y'].split(' '))\n",
    "    check=[]\n",
    "    if len(px.intersection(py)) > 0: \n",
    "        return False\n",
    "    else:\n",
    "        return True"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Get enriched SemMedDB objects for a given search term\n",
    "\n",
    "Starting from a PubMed search, return all SemMedDB subject-predicate-object triples, their enrcichment metrics and publication information "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>query</th>\n",
       "      <th>triple</th>\n",
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       "      <th>subject_type</th>\n",
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       "      <th>0</th>\n",
       "      <td>chronic_kidney_disease</td>\n",
       "      <td>Diabetic Nephropathy:CAUSES:End stage renal fa...</td>\n",
       "      <td>Diabetic Nephropathy</td>\n",
       "      <td>dsyn</td>\n",
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       "      <td>Anemia</td>\n",
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       "      <td>COEXISTS_WITH</td>\n",
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       "      <td>0.000000</td>\n",
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       "      <td>C0022661</td>\n",
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       "      <td>Cardiovascular Diseases</td>\n",
       "      <td>dsyn</td>\n",
       "      <td>C0007222</td>\n",
       "      <td>329</td>\n",
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       "      <td>chronic_kidney_disease</td>\n",
       "      <td>Cardiovascular Diseases:COEXISTS_WITH:Kidney F...</td>\n",
       "      <td>Cardiovascular Diseases</td>\n",
       "      <td>dsyn</td>\n",
       "      <td>C0007222</td>\n",
       "      <td>COEXISTS_WITH</td>\n",
       "      <td>Kidney Failure, Chronic</td>\n",
       "      <td>dsyn</td>\n",
       "      <td>C0022661</td>\n",
       "      <td>318</td>\n",
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       "      <td>82.656402</td>\n",
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       "      <td>Hypertensive disease:COEXISTS_WITH:Kidney Fail...</td>\n",
       "      <td>Hypertensive disease</td>\n",
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       "      <td>C0020538</td>\n",
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       "      <th>11748</th>\n",
       "      <td>chronic_kidney_disease</td>\n",
       "      <td>Dihydrotachysterol:TREATS:Bone Diseases</td>\n",
       "      <td>Dihydrotachysterol</td>\n",
       "      <td>phsu</td>\n",
       "      <td>C0012319</td>\n",
       "      <td>TREATS</td>\n",
       "      <td>Bone Diseases</td>\n",
       "      <td>dsyn</td>\n",
       "      <td>C0005940</td>\n",
       "      <td>2</td>\n",
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       "      <td>2</td>\n",
       "      <td>8295443</td>\n",
       "      <td>83.433317</td>\n",
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       "      <td>951878 907948</td>\n",
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       "      <td>chronic_kidney_disease</td>\n",
       "      <td>Chronic Kidney Insufficiency:COEXISTS_WITH:Uro...</td>\n",
       "      <td>Chronic Kidney Insufficiency</td>\n",
       "      <td>dsyn</td>\n",
       "      <td>C0403447</td>\n",
       "      <td>COEXISTS_WITH</td>\n",
       "      <td>Urolithiasis</td>\n",
       "      <td>dsyn</td>\n",
       "      <td>C0451641</td>\n",
       "      <td>2</td>\n",
       "      <td>99428</td>\n",
       "      <td>2</td>\n",
       "      <td>8295443</td>\n",
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       "      <td>Chronic Kidney Insufficiency</td>\n",
       "      <td>dsyn</td>\n",
       "      <td>C0403447</td>\n",
       "      <td>COEXISTS_WITH</td>\n",
       "      <td>Hyperparathyroidism, Secondary</td>\n",
       "      <td>dsyn</td>\n",
       "      <td>C0020503</td>\n",
       "      <td>2</td>\n",
       "      <td>99428</td>\n",
       "      <td>2</td>\n",
       "      <td>8295443</td>\n",
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       "    <tr>\n",
       "      <th>11751</th>\n",
       "      <td>chronic_kidney_disease</td>\n",
       "      <td>Kidney Failure, Chronic:CAUSES:Zinc deficiency</td>\n",
       "      <td>Kidney Failure, Chronic</td>\n",
       "      <td>dsyn</td>\n",
       "      <td>C0022661</td>\n",
       "      <td>CAUSES</td>\n",
       "      <td>Zinc deficiency</td>\n",
       "      <td>dsyn</td>\n",
       "      <td>C0235950</td>\n",
       "      <td>2</td>\n",
       "      <td>99428</td>\n",
       "      <td>2</td>\n",
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       "    <tr>\n",
       "      <th>11752</th>\n",
       "      <td>chronic_kidney_disease</td>\n",
       "      <td>fenbufen:TREATS:Chronic Disease</td>\n",
       "      <td>fenbufen</td>\n",
       "      <td>phsu</td>\n",
       "      <td>C0060156</td>\n",
       "      <td>TREATS</td>\n",
       "      <td>Chronic Disease</td>\n",
       "      <td>dsyn</td>\n",
       "      <td>C0008679</td>\n",
       "      <td>2</td>\n",
       "      <td>99428</td>\n",
       "      <td>2</td>\n",
       "      <td>8295443</td>\n",
       "      <td>83.433317</td>\n",
       "      <td>0.000828</td>\n",
       "      <td>7111382 7084290</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>11753 rows × 16 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                        query  \\\n",
       "0      chronic_kidney_disease   \n",
       "1      chronic_kidney_disease   \n",
       "2      chronic_kidney_disease   \n",
       "3      chronic_kidney_disease   \n",
       "4      chronic_kidney_disease   \n",
       "...                       ...   \n",
       "11748  chronic_kidney_disease   \n",
       "11749  chronic_kidney_disease   \n",
       "11750  chronic_kidney_disease   \n",
       "11751  chronic_kidney_disease   \n",
       "11752  chronic_kidney_disease   \n",
       "\n",
       "                                                  triple  \\\n",
       "0      Diabetic Nephropathy:CAUSES:End stage renal fa...   \n",
       "1           Anemia:COEXISTS_WITH:Kidney Failure, Chronic   \n",
       "2      Kidney Failure, Chronic:PREDISPOSES:Cardiovasc...   \n",
       "3      Cardiovascular Diseases:COEXISTS_WITH:Kidney F...   \n",
       "4      Hypertensive disease:COEXISTS_WITH:Kidney Fail...   \n",
       "...                                                  ...   \n",
       "11748            Dihydrotachysterol:TREATS:Bone Diseases   \n",
       "11749  Chronic Kidney Insufficiency:COEXISTS_WITH:Uro...   \n",
       "11750  Chronic Kidney Insufficiency:COEXISTS_WITH:Hyp...   \n",
       "11751     Kidney Failure, Chronic:CAUSES:Zinc deficiency   \n",
       "11752                    fenbufen:TREATS:Chronic Disease   \n",
       "\n",
       "                       subject_name subject_type subject_id      predicate  \\\n",
       "0              Diabetic Nephropathy         dsyn   C0011881         CAUSES   \n",
       "1                            Anemia         dsyn   C0002871  COEXISTS_WITH   \n",
       "2           Kidney Failure, Chronic         dsyn   C0022661    PREDISPOSES   \n",
       "3           Cardiovascular Diseases         dsyn   C0007222  COEXISTS_WITH   \n",
       "4              Hypertensive disease         dsyn   C0020538  COEXISTS_WITH   \n",
       "...                             ...          ...        ...            ...   \n",
       "11748            Dihydrotachysterol         phsu   C0012319         TREATS   \n",
       "11749  Chronic Kidney Insufficiency         dsyn   C0403447  COEXISTS_WITH   \n",
       "11750  Chronic Kidney Insufficiency         dsyn   C0403447  COEXISTS_WITH   \n",
       "11751       Kidney Failure, Chronic         dsyn   C0022661         CAUSES   \n",
       "11752                      fenbufen         phsu   C0060156         TREATS   \n",
       "\n",
       "                          object_name object_type object_id  localCount  \\\n",
       "0             End stage renal failure        dsyn  C1261469         389   \n",
       "1             Kidney Failure, Chronic        dsyn  C0022661         357   \n",
       "2             Cardiovascular Diseases        dsyn  C0007222         329   \n",
       "3             Kidney Failure, Chronic        dsyn  C0022661         318   \n",
       "4             Kidney Failure, Chronic        dsyn  C0022661         306   \n",
       "...                               ...         ...       ...         ...   \n",
       "11748                   Bone Diseases        dsyn  C0005940           2   \n",
       "11749                    Urolithiasis        dsyn  C0451641           2   \n",
       "11750  Hyperparathyroidism, Secondary        dsyn  C0020503           2   \n",
       "11751                 Zinc deficiency        dsyn  C0235950           2   \n",
       "11752                 Chronic Disease        dsyn  C0008679           2   \n",
       "\n",
       "       localTotal globalCount  globalTotal       odds      pval  \\\n",
       "0           99428         976      8295443  33.379669  0.000000   \n",
       "1           99428         368      8295443  81.225832  0.000000   \n",
       "2           99428         331      8295443  83.199533  0.000000   \n",
       "3           99428         322      8295443  82.656402  0.000000   \n",
       "4           99428         314      8295443  81.553925  0.000000   \n",
       "...           ...         ...          ...        ...       ...   \n",
       "11748       99428           2      8295443  83.433317  0.000828   \n",
       "11749       99428           2      8295443  83.433317  0.000828   \n",
       "11750       99428           2      8295443  83.433317  0.000828   \n",
       "11751       99428           2      8295443  83.433317  0.000828   \n",
       "11752       99428           2      8295443  83.433317  0.000828   \n",
       "\n",
       "                                                   pmids  \n",
       "0      27275335 29745907 25871838 23816723 30101924 2...  \n",
       "1      24691014 25817226 27742192 30022586 21722599 3...  \n",
       "2      20424360 27865823 18657657 29866459 18987465 1...  \n",
       "3      25923753 18266955 27796755 17198930 25055351 1...  \n",
       "4      1197258 16336577 24770618 24304473 17173252 18...  \n",
       "...                                                  ...  \n",
       "11748                                      951878 907948  \n",
       "11749                                    7052364 1223368  \n",
       "11750                                    5595568 1189399  \n",
       "11751                                            6361778  \n",
       "11752                                    7111382 7084290  \n",
       "\n",
       "[11753 rows x 16 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "query_term='chronic kidney disease'\n",
    "\n",
    "enrich_df = enrich(query_term)\n",
    "enrich_df"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Overlapping terms\n",
    "\n",
    "We can provide two lists of query terms and identify overlapping data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(1817, 32)\n",
      "49 records were found in the same publication\n",
      "(1768, 32)\n"
     ]
    },
    {
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       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>MLH1 gene|MLH1:COEXISTS_WITH:MSH2 gene|MSH2</td>\n",
       "      <td>MLH1 gene|MLH1</td>\n",
       "      <td>gngm</td>\n",
       "      <td>C0879389|4292</td>\n",
       "      <td>COEXISTS_WITH</td>\n",
       "      <td>MSH2 gene|MSH2</td>\n",
       "      <td>gngm</td>\n",
       "      <td>C0879290|4436</td>\n",
       "      <td>52</td>\n",
       "      <td>1969</td>\n",
       "      <td>...</td>\n",
       "      <td>gngm</td>\n",
       "      <td>C0879393|2956</td>\n",
       "      <td>15</td>\n",
       "      <td>630</td>\n",
       "      <td>22</td>\n",
       "      <td>8295443</td>\n",
       "      <td>9196.697339</td>\n",
       "      <td>1.273174e-52</td>\n",
       "      <td>29672549 26657901 22495361 28932927 25106712 2...</td>\n",
       "      <td>hereditary_non-polyposis_colon_cancer</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>MLH1 gene|MLH1:COEXISTS_WITH:MSH2 gene|MSH2</td>\n",
       "      <td>MLH1 gene|MLH1</td>\n",
       "      <td>gngm</td>\n",
       "      <td>C0879389|4292</td>\n",
       "      <td>COEXISTS_WITH</td>\n",
       "      <td>MSH2 gene|MSH2</td>\n",
       "      <td>gngm</td>\n",
       "      <td>C0879290|4436</td>\n",
       "      <td>52</td>\n",
       "      <td>1969</td>\n",
       "      <td>...</td>\n",
       "      <td>dsyn</td>\n",
       "      <td>C0039082</td>\n",
       "      <td>8</td>\n",
       "      <td>630</td>\n",
       "      <td>9</td>\n",
       "      <td>8295443</td>\n",
       "      <td>11854.853876</td>\n",
       "      <td>2.569749e-29</td>\n",
       "      <td>22361722 19900449 26509248 15782118 9538124 16...</td>\n",
       "      <td>hereditary_non-polyposis_colon_cancer</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>MLH1 gene|MLH1:COEXISTS_WITH:MSH2 gene|MSH2</td>\n",
       "      <td>MLH1 gene|MLH1</td>\n",
       "      <td>gngm</td>\n",
       "      <td>C0879389|4292</td>\n",
       "      <td>COEXISTS_WITH</td>\n",
       "      <td>MSH2 gene|MSH2</td>\n",
       "      <td>gngm</td>\n",
       "      <td>C0879290|4436</td>\n",
       "      <td>52</td>\n",
       "      <td>1969</td>\n",
       "      <td>...</td>\n",
       "      <td>dsyn</td>\n",
       "      <td>C0039082</td>\n",
       "      <td>7</td>\n",
       "      <td>630</td>\n",
       "      <td>10</td>\n",
       "      <td>8295443</td>\n",
       "      <td>9320.711236</td>\n",
       "      <td>2.737411e-25</td>\n",
       "      <td>17278092 25319978 25701956 12145848 18709565 2...</td>\n",
       "      <td>hereditary_non-polyposis_colon_cancer</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>MLH1 gene|MLH1:COEXISTS_WITH:MSH2 gene|MSH2</td>\n",
       "      <td>MLH1 gene|MLH1</td>\n",
       "      <td>gngm</td>\n",
       "      <td>C0879389|4292</td>\n",
       "      <td>COEXISTS_WITH</td>\n",
       "      <td>MSH2 gene|MSH2</td>\n",
       "      <td>gngm</td>\n",
       "      <td>C0879290|4436</td>\n",
       "      <td>52</td>\n",
       "      <td>1969</td>\n",
       "      <td>...</td>\n",
       "      <td>gngm</td>\n",
       "      <td>C0879391|5395</td>\n",
       "      <td>4</td>\n",
       "      <td>630</td>\n",
       "      <td>4</td>\n",
       "      <td>8295443</td>\n",
       "      <td>13251.500000</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>25701956 29758216 18781192 26657901</td>\n",
       "      <td>hereditary_non-polyposis_colon_cancer</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>MLH1 gene|MLH1:COEXISTS_WITH:MSH2 gene|MSH2</td>\n",
       "      <td>MLH1 gene|MLH1</td>\n",
       "      <td>gngm</td>\n",
       "      <td>C0879389|4292</td>\n",
       "      <td>COEXISTS_WITH</td>\n",
       "      <td>MSH2 gene|MSH2</td>\n",
       "      <td>gngm</td>\n",
       "      <td>C0879290|4436</td>\n",
       "      <td>52</td>\n",
       "      <td>1969</td>\n",
       "      <td>...</td>\n",
       "      <td>inch</td>\n",
       "      <td>C0170127</td>\n",
       "      <td>4</td>\n",
       "      <td>630</td>\n",
       "      <td>5</td>\n",
       "      <td>8295443</td>\n",
       "      <td>10601.198722</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>30916491 11208710 28646840 18257912</td>\n",
       "      <td>hereditary_non-polyposis_colon_cancer</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1812</th>\n",
       "      <td>Phosphotransferases:COEXISTS_WITH:APC</td>\n",
       "      <td>Phosphotransferases</td>\n",
       "      <td>aapp</td>\n",
       "      <td>C0031727</td>\n",
       "      <td>COEXISTS_WITH</td>\n",
       "      <td>APC</td>\n",
       "      <td>gngm</td>\n",
       "      <td>324</td>\n",
       "      <td>3</td>\n",
       "      <td>21141</td>\n",
       "      <td>...</td>\n",
       "      <td>orch</td>\n",
       "      <td>C0038792</td>\n",
       "      <td>2</td>\n",
       "      <td>630</td>\n",
       "      <td>3</td>\n",
       "      <td>8295443</td>\n",
       "      <td>8806.199575</td>\n",
       "      <td>5.760000e-08</td>\n",
       "      <td>19755659</td>\n",
       "      <td>hereditary_non-polyposis_colon_cancer</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1813</th>\n",
       "      <td>APCS:COEXISTS_WITH:APC</td>\n",
       "      <td>APCS</td>\n",
       "      <td>gngm</td>\n",
       "      <td>325</td>\n",
       "      <td>COEXISTS_WITH</td>\n",
       "      <td>APC</td>\n",
       "      <td>gngm</td>\n",
       "      <td>324</td>\n",
       "      <td>3</td>\n",
       "      <td>21141</td>\n",
       "      <td>...</td>\n",
       "      <td>orch</td>\n",
       "      <td>C0038792</td>\n",
       "      <td>2</td>\n",
       "      <td>630</td>\n",
       "      <td>3</td>\n",
       "      <td>8295443</td>\n",
       "      <td>8806.199575</td>\n",
       "      <td>5.760000e-08</td>\n",
       "      <td>19755659</td>\n",
       "      <td>hereditary_non-polyposis_colon_cancer</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1814</th>\n",
       "      <td>Interleukin-2:INTERACTS_WITH:APC</td>\n",
       "      <td>Interleukin-2</td>\n",
       "      <td>aapp</td>\n",
       "      <td>C0021756</td>\n",
       "      <td>INTERACTS_WITH</td>\n",
       "      <td>APC</td>\n",
       "      <td>gngm</td>\n",
       "      <td>324</td>\n",
       "      <td>3</td>\n",
       "      <td>21141</td>\n",
       "      <td>...</td>\n",
       "      <td>orch</td>\n",
       "      <td>C0038792</td>\n",
       "      <td>2</td>\n",
       "      <td>630</td>\n",
       "      <td>3</td>\n",
       "      <td>8295443</td>\n",
       "      <td>8806.199575</td>\n",
       "      <td>5.760000e-08</td>\n",
       "      <td>19755659</td>\n",
       "      <td>hereditary_non-polyposis_colon_cancer</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1815</th>\n",
       "      <td>CD40 Ligand|CD40LG:STIMULATES:APC</td>\n",
       "      <td>CD40 Ligand|CD40LG</td>\n",
       "      <td>aapp</td>\n",
       "      <td>C0167627|959</td>\n",
       "      <td>STIMULATES</td>\n",
       "      <td>APC</td>\n",
       "      <td>gngm</td>\n",
       "      <td>324</td>\n",
       "      <td>3</td>\n",
       "      <td>21141</td>\n",
       "      <td>...</td>\n",
       "      <td>orch</td>\n",
       "      <td>C0038792</td>\n",
       "      <td>2</td>\n",
       "      <td>630</td>\n",
       "      <td>3</td>\n",
       "      <td>8295443</td>\n",
       "      <td>8806.199575</td>\n",
       "      <td>5.760000e-08</td>\n",
       "      <td>19755659</td>\n",
       "      <td>hereditary_non-polyposis_colon_cancer</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1816</th>\n",
       "      <td>beta catenin:STIMULATES:Oncogenes</td>\n",
       "      <td>beta catenin</td>\n",
       "      <td>aapp</td>\n",
       "      <td>C0105770</td>\n",
       "      <td>STIMULATES</td>\n",
       "      <td>Oncogenes</td>\n",
       "      <td>gngm</td>\n",
       "      <td>C0029016</td>\n",
       "      <td>3</td>\n",
       "      <td>21141</td>\n",
       "      <td>...</td>\n",
       "      <td>gngm</td>\n",
       "      <td>C0079427</td>\n",
       "      <td>3</td>\n",
       "      <td>630</td>\n",
       "      <td>65</td>\n",
       "      <td>8295443</td>\n",
       "      <td>610.627751</td>\n",
       "      <td>2.180000e-08</td>\n",
       "      <td>1580606 8600059 8898451</td>\n",
       "      <td>hereditary_non-polyposis_colon_cancer</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1768 rows × 32 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                         triple_x       subject_name_x  \\\n",
       "1     MLH1 gene|MLH1:COEXISTS_WITH:MSH2 gene|MSH2       MLH1 gene|MLH1   \n",
       "2     MLH1 gene|MLH1:COEXISTS_WITH:MSH2 gene|MSH2       MLH1 gene|MLH1   \n",
       "3     MLH1 gene|MLH1:COEXISTS_WITH:MSH2 gene|MSH2       MLH1 gene|MLH1   \n",
       "5     MLH1 gene|MLH1:COEXISTS_WITH:MSH2 gene|MSH2       MLH1 gene|MLH1   \n",
       "6     MLH1 gene|MLH1:COEXISTS_WITH:MSH2 gene|MSH2       MLH1 gene|MLH1   \n",
       "...                                           ...                  ...   \n",
       "1812        Phosphotransferases:COEXISTS_WITH:APC  Phosphotransferases   \n",
       "1813                       APCS:COEXISTS_WITH:APC                 APCS   \n",
       "1814             Interleukin-2:INTERACTS_WITH:APC        Interleukin-2   \n",
       "1815            CD40 Ligand|CD40LG:STIMULATES:APC   CD40 Ligand|CD40LG   \n",
       "1816            beta catenin:STIMULATES:Oncogenes         beta catenin   \n",
       "\n",
       "     subject_type_x   subject_id_x     predicate_x   object_name_x  \\\n",
       "1              gngm  C0879389|4292   COEXISTS_WITH  MSH2 gene|MSH2   \n",
       "2              gngm  C0879389|4292   COEXISTS_WITH  MSH2 gene|MSH2   \n",
       "3              gngm  C0879389|4292   COEXISTS_WITH  MSH2 gene|MSH2   \n",
       "5              gngm  C0879389|4292   COEXISTS_WITH  MSH2 gene|MSH2   \n",
       "6              gngm  C0879389|4292   COEXISTS_WITH  MSH2 gene|MSH2   \n",
       "...             ...            ...             ...             ...   \n",
       "1812           aapp       C0031727   COEXISTS_WITH             APC   \n",
       "1813           gngm            325   COEXISTS_WITH             APC   \n",
       "1814           aapp       C0021756  INTERACTS_WITH             APC   \n",
       "1815           aapp   C0167627|959      STIMULATES             APC   \n",
       "1816           aapp       C0105770      STIMULATES       Oncogenes   \n",
       "\n",
       "     object_type_x    object_id_x  localCount_x  localTotal_x  ...  \\\n",
       "1             gngm  C0879290|4436            52          1969  ...   \n",
       "2             gngm  C0879290|4436            52          1969  ...   \n",
       "3             gngm  C0879290|4436            52          1969  ...   \n",
       "5             gngm  C0879290|4436            52          1969  ...   \n",
       "6             gngm  C0879290|4436            52          1969  ...   \n",
       "...            ...            ...           ...           ...  ...   \n",
       "1812          gngm            324             3         21141  ...   \n",
       "1813          gngm            324             3         21141  ...   \n",
       "1814          gngm            324             3         21141  ...   \n",
       "1815          gngm            324             3         21141  ...   \n",
       "1816          gngm       C0029016             3         21141  ...   \n",
       "\n",
       "      object_type_y    object_id_y  localCount_y  localTotal_y globalCount_y  \\\n",
       "1              gngm  C0879393|2956            15           630            22   \n",
       "2              dsyn       C0039082             8           630             9   \n",
       "3              dsyn       C0039082             7           630            10   \n",
       "5              gngm  C0879391|5395             4           630             4   \n",
       "6              inch       C0170127             4           630             5   \n",
       "...             ...            ...           ...           ...           ...   \n",
       "1812           orch       C0038792             2           630             3   \n",
       "1813           orch       C0038792             2           630             3   \n",
       "1814           orch       C0038792             2           630             3   \n",
       "1815           orch       C0038792             2           630             3   \n",
       "1816           gngm       C0079427             3           630            65   \n",
       "\n",
       "     globalTotal_y        odds_y        pval_y  \\\n",
       "1          8295443   9196.697339  1.273174e-52   \n",
       "2          8295443  11854.853876  2.569749e-29   \n",
       "3          8295443   9320.711236  2.737411e-25   \n",
       "5          8295443  13251.500000  0.000000e+00   \n",
       "6          8295443  10601.198722  0.000000e+00   \n",
       "...            ...           ...           ...   \n",
       "1812       8295443   8806.199575  5.760000e-08   \n",
       "1813       8295443   8806.199575  5.760000e-08   \n",
       "1814       8295443   8806.199575  5.760000e-08   \n",
       "1815       8295443   8806.199575  5.760000e-08   \n",
       "1816       8295443    610.627751  2.180000e-08   \n",
       "\n",
       "                                                pmids_y  \\\n",
       "1     29672549 26657901 22495361 28932927 25106712 2...   \n",
       "2     22361722 19900449 26509248 15782118 9538124 16...   \n",
       "3     17278092 25319978 25701956 12145848 18709565 2...   \n",
       "5                   25701956 29758216 18781192 26657901   \n",
       "6                   30916491 11208710 28646840 18257912   \n",
       "...                                                 ...   \n",
       "1812                                           19755659   \n",
       "1813                                           19755659   \n",
       "1814                                           19755659   \n",
       "1815                                           19755659   \n",
       "1816                            1580606 8600059 8898451   \n",
       "\n",
       "                                      set_y  \n",
       "1     hereditary_non-polyposis_colon_cancer  \n",
       "2     hereditary_non-polyposis_colon_cancer  \n",
       "3     hereditary_non-polyposis_colon_cancer  \n",
       "5     hereditary_non-polyposis_colon_cancer  \n",
       "6     hereditary_non-polyposis_colon_cancer  \n",
       "...                                     ...  \n",
       "1812  hereditary_non-polyposis_colon_cancer  \n",
       "1813  hereditary_non-polyposis_colon_cancer  \n",
       "1814  hereditary_non-polyposis_colon_cancer  \n",
       "1815  hereditary_non-polyposis_colon_cancer  \n",
       "1816  hereditary_non-polyposis_colon_cancer  \n",
       "\n",
       "[1768 rows x 32 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "x=['MLH1','MSH2','MLH3','MSH6','PMS1','PMS2','APC']\n",
    "y=['Hereditary non-polyposis colon cancer']\n",
    "\n",
    "overlap_df = overlap(x,y)\n",
    "print(overlap_df.shape)\n",
    "\n",
    "#remove records found in the same publication\n",
    "pub_filter=overlap_df.apply(pub_check,axis=1)\n",
    "pub_removed = overlap_df.shape[0]-pub_filter.sum()\n",
    "print(pub_removed,'records were found in the same publication')\n",
    "overlap_df=overlap_df[pub_filter]\n",
    "print(overlap_df.shape)\n",
    "overlap_df"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Look at the overlapping data in more detail"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "object_type_x  object_name_x       \n",
       "aapp           MLH1 gene|MLH1           78\n",
       "               beta catenin             36\n",
       "               APC                       2\n",
       "gngm           MLH1 gene|MLH1          668\n",
       "               MSH2 gene|MSH2          661\n",
       "               MSH6 gene|MSH6          129\n",
       "               PMS2 gene|PMS2           96\n",
       "               APC                      64\n",
       "               beta catenin             16\n",
       "               BRAF gene|BRAF            8\n",
       "               DNA Repair Gene           4\n",
       "               TACSTD2 gene|TACSTD2      3\n",
       "               Oncogenes                 1\n",
       "orch           Sulindac                  2\n",
       "Name: object_name_x, dtype: int64"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "overlap_counts = overlap_df.groupby('object_type_x')['object_name_x'].value_counts()\n",
    "overlap_counts"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Publicaton data\n",
    "\n",
    "We can retrive the SemMedDB data for a give PubMed ID"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>PREDICATION_ID</th>\n",
       "      <th>SENTENCE_ID</th>\n",
       "      <th>PMID</th>\n",
       "      <th>PREDICATE</th>\n",
       "      <th>SUBJECT_CUI</th>\n",
       "      <th>SUBJECT_NAME</th>\n",
       "      <th>SUBJECT_SEMTYPE</th>\n",
       "      <th>SUBJECT_NOVELTY</th>\n",
       "      <th>OBJECT_CUI</th>\n",
       "      <th>OBJECT_NAME</th>\n",
       "      <th>...</th>\n",
       "      <th>NUMBER</th>\n",
       "      <th>SENT_START_INDEX</th>\n",
       "      <th>SENT_END_INDEX</th>\n",
       "      <th>SECTION_HEADER</th>\n",
       "      <th>NORMALIZED_SECTION_HEADER</th>\n",
       "      <th>SENTENCE</th>\n",
       "      <th>ISSN</th>\n",
       "      <th>DP</th>\n",
       "      <th>EDAT</th>\n",
       "      <th>PYEAR</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>131291235</td>\n",
       "      <td>124272128</td>\n",
       "      <td>19755659</td>\n",
       "      <td>INTERACTS_WITH</td>\n",
       "      <td>324</td>\n",
       "      <td>APC</td>\n",
       "      <td>gngm</td>\n",
       "      <td>1</td>\n",
       "      <td>C0038792</td>\n",
       "      <td>Sulindac</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>21</td>\n",
       "      <td>126</td>\n",
       "      <td>\"\"\"\"\"\"</td>\n",
       "      <td>\"\"\"\"\"\"</td>\n",
       "      <td>Sulindac effects on inflammation and tumorigen...</td>\n",
       "      <td>1460-2180</td>\n",
       "      <td>2009 Nov</td>\n",
       "      <td>2009-9-17</td>\n",
       "      <td>2009</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>131291271</td>\n",
       "      <td>124272128</td>\n",
       "      <td>19755659</td>\n",
       "      <td>INTERACTS_WITH</td>\n",
       "      <td>C0879389|4292</td>\n",
       "      <td>MLH1 gene|MLH1</td>\n",
       "      <td>gngm</td>\n",
       "      <td>1</td>\n",
       "      <td>C0038792</td>\n",
       "      <td>Sulindac</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>21</td>\n",
       "      <td>126</td>\n",
       "      <td>\"\"\"\"\"\"</td>\n",
       "      <td>\"\"\"\"\"\"</td>\n",
       "      <td>Sulindac effects on inflammation and tumorigen...</td>\n",
       "      <td>1460-2180</td>\n",
       "      <td>2009 Nov</td>\n",
       "      <td>2009-9-17</td>\n",
       "      <td>2009</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>131291696</td>\n",
       "      <td>124272130</td>\n",
       "      <td>19755659</td>\n",
       "      <td>INTERACTS_WITH</td>\n",
       "      <td>324</td>\n",
       "      <td>APC</td>\n",
       "      <td>gngm</td>\n",
       "      <td>1</td>\n",
       "      <td>C0038792</td>\n",
       "      <td>Sulindac</td>\n",
       "      <td>...</td>\n",
       "      <td>2</td>\n",
       "      <td>367</td>\n",
       "      <td>802</td>\n",
       "      <td>\"\"\"\"\"\"</td>\n",
       "      <td>\"\"\"\"\"\"</td>\n",
       "      <td>To further explore intestinal regional respons...</td>\n",
       "      <td>1460-2180</td>\n",
       "      <td>2009 Nov</td>\n",
       "      <td>2009-9-17</td>\n",
       "      <td>2009</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>3 rows × 24 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "  PREDICATION_ID SENTENCE_ID      PMID       PREDICATE    SUBJECT_CUI  \\\n",
       "0      131291235   124272128  19755659  INTERACTS_WITH            324   \n",
       "1      131291271   124272128  19755659  INTERACTS_WITH  C0879389|4292   \n",
       "2      131291696   124272130  19755659  INTERACTS_WITH            324   \n",
       "\n",
       "     SUBJECT_NAME SUBJECT_SEMTYPE  SUBJECT_NOVELTY OBJECT_CUI OBJECT_NAME  \\\n",
       "0             APC            gngm                1   C0038792    Sulindac   \n",
       "1  MLH1 gene|MLH1            gngm                1   C0038792    Sulindac   \n",
       "2             APC            gngm                1   C0038792    Sulindac   \n",
       "\n",
       "   ... NUMBER  SENT_START_INDEX SENT_END_INDEX SECTION_HEADER  \\\n",
       "0  ...      1                21            126         \"\"\"\"\"\"   \n",
       "1  ...      1                21            126         \"\"\"\"\"\"   \n",
       "2  ...      2               367            802         \"\"\"\"\"\"   \n",
       "\n",
       "  NORMALIZED_SECTION_HEADER  \\\n",
       "0                    \"\"\"\"\"\"   \n",
       "1                    \"\"\"\"\"\"   \n",
       "2                    \"\"\"\"\"\"   \n",
       "\n",
       "                                            SENTENCE       ISSN        DP  \\\n",
       "0  Sulindac effects on inflammation and tumorigen...  1460-2180  2009 Nov   \n",
       "1  Sulindac effects on inflammation and tumorigen...  1460-2180  2009 Nov   \n",
       "2  To further explore intestinal regional respons...  1460-2180  2009 Nov   \n",
       "\n",
       "        EDAT PYEAR  \n",
       "0  2009-9-17  2009  \n",
       "1  2009-9-17  2009  \n",
       "2  2009-9-17  2009  \n",
       "\n",
       "[3 rows x 24 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pmid = '19755659'\n",
    "pub_df = sentence(pmid)\n",
    "pub_df"
   ]
  }
 ],
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