demo_med_pipeline.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from glob import glob\n",
    "import pandas as pd\n",
    "import re\n",
    "from pprint import pprint\n",
    "import pkg_resources\n",
    "\n",
    "from pymedextcore.document import Document\n",
    "from pymedext_eds.annotators import Endlines, SentenceTokenizer, SectionSplitter, rawtext_loader\n",
    "from pymedext_eds.med import MedicationAnnotator, MedicationNormalizer"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "models_param = [{'tagger_path':'/export/home/cse180025/prod_information_extraction/data/models/apmed4/entities/final-model.pt' ,\n",
    "                'tag_name': 'entity_pred' },\n",
    "                {'tagger_path':'/export/home/cse180025/prod_information_extraction/data/models/apmed4/events/final-model.pt' ,\n",
    "                'tag_name': 'event_pred' },\n",
    "               {'tagger_path': \"/export/home/cse180025/prod_information_extraction/data/models/apmed4/drugblob/final-model.pt\",\n",
    "                'tag_name': 'drugblob_pred'}]\n",
    "\n",
    "data_path = pkg_resources.resource_filename('pymedext_eds', 'data/romedi')\n",
    "romedi_path = glob(data_path + '/*.p')[0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2020-11-05 15:02:05,023 loading file /export/home/cse180025/prod_information_extraction/data/models/apmed4/entities/final-model.pt\n",
      "2020-11-05 15:02:09,402 loading file /export/home/cse180025/prod_information_extraction/data/models/apmed4/events/final-model.pt\n",
      "2020-11-05 15:02:11,062 loading file /export/home/cse180025/prod_information_extraction/data/models/apmed4/drugblob/final-model.pt\n"
     ]
    }
   ],
   "source": [
    "endlines = Endlines([\"raw_text\"], \"clean_text\", ID=\"endlines\")\n",
    "sections = SectionSplitter(['clean_text'], \"section\", ID= 'sections')\n",
    "sentenceSplitter = SentenceTokenizer([\"section\"],\"sentence\", ID=\"sentences\")\n",
    "med = MedicationAnnotator(['sentence'], 'med', ID='med:v2', models_param=models_param,  device='cuda:1')\n",
    "norm = MedicationNormalizer(['ENT/DRUG','ENT/CLASS'], 'normalized_mention', ID='norm',romedi_path= romedi_path)\n",
    "\n",
    "pipeline = [endlines,sections, sentenceSplitter, med, norm]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "data_path = pkg_resources.resource_filename('pymedext_eds', 'data/demo')\n",
    "file_list = glob(data_path + '/*.txt')\n",
    "\n",
    "docs = [rawtext_loader(x) for x in file_list]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Ignore 2 sentence(s) with no tokens.\n"
     ]
    }
   ],
   "source": [
    "for doc in docs:\n",
    "    doc.annotate(pipeline)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
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       "      <td>cas2</td>\n",
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       "      <td>Le 9 décembre 2010, une femme de 79 ans reçoit...</td>\n",
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       "      <td>None</td>\n",
       "      <td>section='head',score='0.9963575005531311',snip...</td>\n",
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       "      <th>1</th>\n",
       "      <td>None</td>\n",
       "      <td>cas2</td>\n",
       "      <td>cas2</td>\n",
       "      <td>head</td>\n",
       "      <td>Un traitement par des soins locaux avec des p...</td>\n",
       "      <td>1254</td>\n",
       "      <td>1264</td>\n",
       "      <td>tulle gras</td>\n",
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       "      <td>ATC</td>\n",
       "      <td>medext_v3</td>\n",
       "      <td>2020-11-05</td>\n",
       "      <td>2020-11-05 15:04:55</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>section='head',score='0.9664367139339447'</td>\n",
       "      <td>automated</td>\n",
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       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>None</td>\n",
       "      <td>cas2</td>\n",
       "      <td>cas2</td>\n",
       "      <td>head</td>\n",
       "      <td>Un traitement par des soins locaux avec des p...</td>\n",
       "      <td>1294</td>\n",
       "      <td>1302</td>\n",
       "      <td>Plurexid</td>\n",
       "      <td>D08AC02</td>\n",
       "      <td>ATC</td>\n",
       "      <td>medext_v3</td>\n",
       "      <td>2020-11-05</td>\n",
       "      <td>2020-11-05 15:04:55</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>section='head',score='0.9969384670257568',ATC_...</td>\n",
       "      <td>automated</td>\n",
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       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>None</td>\n",
       "      <td>cas2</td>\n",
       "      <td>cas2</td>\n",
       "      <td>head</td>\n",
       "      <td>Le 17 février 2014, un traitement par Augment...</td>\n",
       "      <td>2362</td>\n",
       "      <td>2371</td>\n",
       "      <td>Augmentin</td>\n",
       "      <td>J01CR02</td>\n",
       "      <td>ATC</td>\n",
       "      <td>medext_v3</td>\n",
       "      <td>2020-11-05</td>\n",
       "      <td>2020-11-05 15:04:55</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>section='head',score='0.9999349117279053',ATC_...</td>\n",
       "      <td>automated</td>\n",
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       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>None</td>\n",
       "      <td>cas2</td>\n",
       "      <td>cas2</td>\n",
       "      <td>head</td>\n",
       "      <td>En raison d'une diarrhée, l’Augmentin® est re...</td>\n",
       "      <td>2583</td>\n",
       "      <td>2591</td>\n",
       "      <td>Solupred</td>\n",
       "      <td>H02AB06</td>\n",
       "      <td>ATC</td>\n",
       "      <td>medext_v3</td>\n",
       "      <td>2020-11-05</td>\n",
       "      <td>2020-11-05 15:04:55</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>section='head',score='0.9998010993003845',ATC_...</td>\n",
       "      <td>automated</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>None</td>\n",
       "      <td>cas2</td>\n",
       "      <td>cas2</td>\n",
       "      <td>head</td>\n",
       "      <td>En raison d'une diarrhée, l’Augmentin® est re...</td>\n",
       "      <td>2509</td>\n",
       "      <td>2518</td>\n",
       "      <td>Rocéphine</td>\n",
       "      <td>J01DD04</td>\n",
       "      <td>ATC</td>\n",
       "      <td>medext_v3</td>\n",
       "      <td>2020-11-05</td>\n",
       "      <td>2020-11-05 15:04:55</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>section='head',score='0.9999445676803589',ENT/...</td>\n",
       "      <td>automated</td>\n",
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       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>None</td>\n",
       "      <td>cas2</td>\n",
       "      <td>cas2</td>\n",
       "      <td>head</td>\n",
       "      <td>Le 28 février, de l'Oroken® est prescrit en a...</td>\n",
       "      <td>2687</td>\n",
       "      <td>2696</td>\n",
       "      <td>Pulmicort</td>\n",
       "      <td>R03BA02</td>\n",
       "      <td>ATC</td>\n",
       "      <td>medext_v3</td>\n",
       "      <td>2020-11-05</td>\n",
       "      <td>2020-11-05 15:04:55</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>section='head',score='0.9989744424819946',ATC_...</td>\n",
       "      <td>automated</td>\n",
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       "      <th>7</th>\n",
       "      <td>None</td>\n",
       "      <td>cas2</td>\n",
       "      <td>cas2</td>\n",
       "      <td>head</td>\n",
       "      <td>Sur la fiche d’admission remplie par le médec...</td>\n",
       "      <td>3549</td>\n",
       "      <td>3559</td>\n",
       "      <td>Pyostacine</td>\n",
       "      <td>J01FG01</td>\n",
       "      <td>ATC</td>\n",
       "      <td>medext_v3</td>\n",
       "      <td>2020-11-05</td>\n",
       "      <td>2020-11-05 15:04:55</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>section='head',score='0.8990024328231812',ATC_...</td>\n",
       "      <td>automated</td>\n",
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       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>None</td>\n",
       "      <td>cas2</td>\n",
       "      <td>cas2</td>\n",
       "      <td>head</td>\n",
       "      <td>Augmentin</td>\n",
       "      <td>3562</td>\n",
       "      <td>3571</td>\n",
       "      <td>Augmentin</td>\n",
       "      <td>J01CR02</td>\n",
       "      <td>ATC</td>\n",
       "      <td>medext_v3</td>\n",
       "      <td>2020-11-05</td>\n",
       "      <td>2020-11-05 15:04:55</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>section='head',score='0.9985721111297607',ATC_...</td>\n",
       "      <td>automated</td>\n",
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       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>None</td>\n",
       "      <td>cas2</td>\n",
       "      <td>cas2</td>\n",
       "      <td>head</td>\n",
       "      <td>Après la réalisation de prélèvements bactério...</td>\n",
       "      <td>4041</td>\n",
       "      <td>4050</td>\n",
       "      <td>Rocéphine</td>\n",
       "      <td>J01DD04</td>\n",
       "      <td>ATC</td>\n",
       "      <td>medext_v3</td>\n",
       "      <td>2020-11-05</td>\n",
       "      <td>2020-11-05 15:04:55</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>section='head',score='0.9982656836509705',ATC_...</td>\n",
       "      <td>automated</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>None</td>\n",
       "      <td>cas2</td>\n",
       "      <td>cas2</td>\n",
       "      <td>head</td>\n",
       "      <td>Après la réalisation de prélèvements bactério...</td>\n",
       "      <td>4055</td>\n",
       "      <td>4065</td>\n",
       "      <td>Pyostacine</td>\n",
       "      <td>J01FG01</td>\n",
       "      <td>ATC</td>\n",
       "      <td>medext_v3</td>\n",
       "      <td>2020-11-05</td>\n",
       "      <td>2020-11-05 15:04:55</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>section='head',score='0.9991045594215393',ATC_...</td>\n",
       "      <td>automated</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>None</td>\n",
       "      <td>cas2</td>\n",
       "      <td>cas2</td>\n",
       "      <td>head</td>\n",
       "      <td>La patiente est transférée en réanimation ave...</td>\n",
       "      <td>4292</td>\n",
       "      <td>4305</td>\n",
       "      <td>noradrenaline</td>\n",
       "      <td>C01CA03</td>\n",
       "      <td>ATC</td>\n",
       "      <td>medext_v3</td>\n",
       "      <td>2020-11-05</td>\n",
       "      <td>2020-11-05 15:04:55</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>section='head',score='0.9997856020927429',ENT/...</td>\n",
       "      <td>automated</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>None</td>\n",
       "      <td>cas2</td>\n",
       "      <td>cas2</td>\n",
       "      <td>head</td>\n",
       "      <td>Mise sous Tazocilline® et Zyvoxi®</td>\n",
       "      <td>4355</td>\n",
       "      <td>4366</td>\n",
       "      <td>Tazocilline</td>\n",
       "      <td>J01CR05</td>\n",
       "      <td>ATC</td>\n",
       "      <td>medext_v3</td>\n",
       "      <td>2020-11-05</td>\n",
       "      <td>2020-11-05 15:04:55</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>section='head',score='0.9998668432235718',ATC_...</td>\n",
       "      <td>automated</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>None</td>\n",
       "      <td>cas2</td>\n",
       "      <td>cas2</td>\n",
       "      <td>head</td>\n",
       "      <td>Mise sous Tazocilline® et Zyvoxi®</td>\n",
       "      <td>4371</td>\n",
       "      <td>4378</td>\n",
       "      <td>Zyvoxi ®</td>\n",
       "      <td>None</td>\n",
       "      <td>ATC</td>\n",
       "      <td>medext_v3</td>\n",
       "      <td>2020-11-05</td>\n",
       "      <td>2020-11-05 15:04:55</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>section='head',score='0.9040422439575195'</td>\n",
       "      <td>automated</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>None</td>\n",
       "      <td>cas2</td>\n",
       "      <td>cas2</td>\n",
       "      <td>head</td>\n",
       "      <td>Le courrier de sortie de réanimation conclue ...</td>\n",
       "      <td>5133</td>\n",
       "      <td>5143</td>\n",
       "      <td>Pyostacine</td>\n",
       "      <td>J01FG01</td>\n",
       "      <td>ATC</td>\n",
       "      <td>medext_v3</td>\n",
       "      <td>2020-11-05</td>\n",
       "      <td>2020-11-05 15:04:55</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>section='head',score='0.9988917708396912',ATC_...</td>\n",
       "      <td>automated</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>None</td>\n",
       "      <td>cas2</td>\n",
       "      <td>cas2</td>\n",
       "      <td>head</td>\n",
       "      <td>A l’admission au CHU, la patiente était confu...</td>\n",
       "      <td>5397</td>\n",
       "      <td>5410</td>\n",
       "      <td>noradrénaline</td>\n",
       "      <td>C01CA03</td>\n",
       "      <td>ATC</td>\n",
       "      <td>medext_v3</td>\n",
       "      <td>2020-11-05</td>\n",
       "      <td>2020-11-05 15:04:55</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>section='head',score='0.999586284160614',ENT/R...</td>\n",
       "      <td>automated</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>None</td>\n",
       "      <td>cas2</td>\n",
       "      <td>cas2</td>\n",
       "      <td>head</td>\n",
       "      <td>Poursuite du traitement par Tazocilline® et Z...</td>\n",
       "      <td>5676</td>\n",
       "      <td>5687</td>\n",
       "      <td>Tazocilline</td>\n",
       "      <td>J01CR05</td>\n",
       "      <td>ATC</td>\n",
       "      <td>medext_v3</td>\n",
       "      <td>2020-11-05</td>\n",
       "      <td>2020-11-05 15:04:55</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>section='head',score='0.9997614026069641',ATC_...</td>\n",
       "      <td>automated</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>None</td>\n",
       "      <td>cas2</td>\n",
       "      <td>cas2</td>\n",
       "      <td>head</td>\n",
       "      <td>Poursuite du traitement par Tazocilline® et Z...</td>\n",
       "      <td>5692</td>\n",
       "      <td>5699</td>\n",
       "      <td>Zyvoxid</td>\n",
       "      <td>J01XX08</td>\n",
       "      <td>ATC</td>\n",
       "      <td>medext_v3</td>\n",
       "      <td>2020-11-05</td>\n",
       "      <td>2020-11-05 15:04:55</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>section='head',score='0.9998646974563599',snip...</td>\n",
       "      <td>automated</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>None</td>\n",
       "      <td>cas2</td>\n",
       "      <td>cas2</td>\n",
       "      <td>head</td>\n",
       "      <td>Au médecin traitant, il était reproché l'omis...</td>\n",
       "      <td>6469</td>\n",
       "      <td>6479</td>\n",
       "      <td>Pyostacine</td>\n",
       "      <td>J01FG01</td>\n",
       "      <td>ATC</td>\n",
       "      <td>medext_v3</td>\n",
       "      <td>2020-11-05</td>\n",
       "      <td>2020-11-05 15:04:55</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>section='head',score='0.9986792206764221',ATC_...</td>\n",
       "      <td>automated</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>None</td>\n",
       "      <td>cas2</td>\n",
       "      <td>cas2</td>\n",
       "      <td>head</td>\n",
       "      <td>Allergie à un antibiotique, lequel</td>\n",
       "      <td>3588</td>\n",
       "      <td>3600</td>\n",
       "      <td>antibiotique</td>\n",
       "      <td>J04AB</td>\n",
       "      <td>ATC</td>\n",
       "      <td>medext_v3</td>\n",
       "      <td>2020-11-05</td>\n",
       "      <td>2020-11-05 15:04:55</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>section='head',score='0.9984001517295837',ATC_...</td>\n",
       "      <td>automated</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>None</td>\n",
       "      <td>cas2</td>\n",
       "      <td>cas2</td>\n",
       "      <td>head</td>\n",
       "      <td>Sur une observation informatisée saisie le mê...</td>\n",
       "      <td>3734</td>\n",
       "      <td>3746</td>\n",
       "      <td>antibiotique</td>\n",
       "      <td>J04AB</td>\n",
       "      <td>ATC</td>\n",
       "      <td>medext_v3</td>\n",
       "      <td>2020-11-05</td>\n",
       "      <td>2020-11-05 15:04:55</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>section='head',score='0.9977784752845764',ATC_...</td>\n",
       "      <td>automated</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>None</td>\n",
       "      <td>cas2</td>\n",
       "      <td>cas2</td>\n",
       "      <td>head</td>\n",
       "      <td>Poursuite du traitement par Tazocilline® et Z...</td>\n",
       "      <td>5734</td>\n",
       "      <td>5745</td>\n",
       "      <td>antalgiques</td>\n",
       "      <td>N02A</td>\n",
       "      <td>ATC</td>\n",
       "      <td>medext_v3</td>\n",
       "      <td>2020-11-05</td>\n",
       "      <td>2020-11-05 15:04:55</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>section='head',score='0.9606321454048157',ATC_...</td>\n",
       "      <td>automated</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   note_nlp_id note_id person_id section_concept_id  \\\n",
       "0         None    cas2      cas2               head   \n",
       "1         None    cas2      cas2               head   \n",
       "2         None    cas2      cas2               head   \n",
       "3         None    cas2      cas2               head   \n",
       "4         None    cas2      cas2               head   \n",
       "5         None    cas2      cas2               head   \n",
       "6         None    cas2      cas2               head   \n",
       "7         None    cas2      cas2               head   \n",
       "8         None    cas2      cas2               head   \n",
       "9         None    cas2      cas2               head   \n",
       "10        None    cas2      cas2               head   \n",
       "11        None    cas2      cas2               head   \n",
       "12        None    cas2      cas2               head   \n",
       "13        None    cas2      cas2               head   \n",
       "14        None    cas2      cas2               head   \n",
       "15        None    cas2      cas2               head   \n",
       "16        None    cas2      cas2               head   \n",
       "17        None    cas2      cas2               head   \n",
       "18        None    cas2      cas2               head   \n",
       "19        None    cas2      cas2               head   \n",
       "20        None    cas2      cas2               head   \n",
       "21        None    cas2      cas2               head   \n",
       "\n",
       "                                              snippet  offset_begin  \\\n",
       "0   Le 9 décembre 2010, une femme de 79 ans reçoit...            65   \n",
       "1    Un traitement par des soins locaux avec des p...          1254   \n",
       "2    Un traitement par des soins locaux avec des p...          1294   \n",
       "3    Le 17 février 2014, un traitement par Augment...          2362   \n",
       "4    En raison d'une diarrhée, l’Augmentin® est re...          2583   \n",
       "5    En raison d'une diarrhée, l’Augmentin® est re...          2509   \n",
       "6    Le 28 février, de l'Oroken® est prescrit en a...          2687   \n",
       "7    Sur la fiche d’admission remplie par le médec...          3549   \n",
       "8                                          Augmentin           3562   \n",
       "9    Après la réalisation de prélèvements bactério...          4041   \n",
       "10   Après la réalisation de prélèvements bactério...          4055   \n",
       "11   La patiente est transférée en réanimation ave...          4292   \n",
       "12                  Mise sous Tazocilline® et Zyvoxi®          4355   \n",
       "13                  Mise sous Tazocilline® et Zyvoxi®          4371   \n",
       "14   Le courrier de sortie de réanimation conclue ...          5133   \n",
       "15   A l’admission au CHU, la patiente était confu...          5397   \n",
       "16   Poursuite du traitement par Tazocilline® et Z...          5676   \n",
       "17   Poursuite du traitement par Tazocilline® et Z...          5692   \n",
       "18   Au médecin traitant, il était reproché l'omis...          6469   \n",
       "19                Allergie à un antibiotique, lequel           3588   \n",
       "20   Sur une observation informatisée saisie le mê...          3734   \n",
       "21   Poursuite du traitement par Tazocilline® et Z...          5734   \n",
       "\n",
       "    offset_end lexical_variant note_nlp_concept_id note_nlp_source_concept_id  \\\n",
       "0           75      Pyostacine             J01FG01                        ATC   \n",
       "1         1264      tulle gras                None                        ATC   \n",
       "2         1302        Plurexid             D08AC02                        ATC   \n",
       "3         2371       Augmentin             J01CR02                        ATC   \n",
       "4         2591        Solupred             H02AB06                        ATC   \n",
       "5         2518       Rocéphine             J01DD04                        ATC   \n",
       "6         2696       Pulmicort             R03BA02                        ATC   \n",
       "7         3559      Pyostacine             J01FG01                        ATC   \n",
       "8         3571       Augmentin             J01CR02                        ATC   \n",
       "9         4050       Rocéphine             J01DD04                        ATC   \n",
       "10        4065      Pyostacine             J01FG01                        ATC   \n",
       "11        4305   noradrenaline             C01CA03                        ATC   \n",
       "12        4366     Tazocilline             J01CR05                        ATC   \n",
       "13        4378        Zyvoxi ®                None                        ATC   \n",
       "14        5143      Pyostacine             J01FG01                        ATC   \n",
       "15        5410   noradrénaline             C01CA03                        ATC   \n",
       "16        5687     Tazocilline             J01CR05                        ATC   \n",
       "17        5699         Zyvoxid             J01XX08                        ATC   \n",
       "18        6479      Pyostacine             J01FG01                        ATC   \n",
       "19        3600    antibiotique               J04AB                        ATC   \n",
       "20        3746    antibiotique               J04AB                        ATC   \n",
       "21        5745     antalgiques                N02A                        ATC   \n",
       "\n",
       "   nlp_system    nlp_date         nlp_datetime term_exists term_temporal  \\\n",
       "0   medext_v3  2020-11-05  2020-11-05 15:04:55        None          None   \n",
       "1   medext_v3  2020-11-05  2020-11-05 15:04:55        None          None   \n",
       "2   medext_v3  2020-11-05  2020-11-05 15:04:55        None          None   \n",
       "3   medext_v3  2020-11-05  2020-11-05 15:04:55        None          None   \n",
       "4   medext_v3  2020-11-05  2020-11-05 15:04:55        None          None   \n",
       "5   medext_v3  2020-11-05  2020-11-05 15:04:55        None          None   \n",
       "6   medext_v3  2020-11-05  2020-11-05 15:04:55        None          None   \n",
       "7   medext_v3  2020-11-05  2020-11-05 15:04:55        None          None   \n",
       "8   medext_v3  2020-11-05  2020-11-05 15:04:55        None          None   \n",
       "9   medext_v3  2020-11-05  2020-11-05 15:04:55        None          None   \n",
       "10  medext_v3  2020-11-05  2020-11-05 15:04:55        None          None   \n",
       "11  medext_v3  2020-11-05  2020-11-05 15:04:55        None          None   \n",
       "12  medext_v3  2020-11-05  2020-11-05 15:04:55        None          None   \n",
       "13  medext_v3  2020-11-05  2020-11-05 15:04:55        None          None   \n",
       "14  medext_v3  2020-11-05  2020-11-05 15:04:55        None          None   \n",
       "15  medext_v3  2020-11-05  2020-11-05 15:04:55        None          None   \n",
       "16  medext_v3  2020-11-05  2020-11-05 15:04:55        None          None   \n",
       "17  medext_v3  2020-11-05  2020-11-05 15:04:55        None          None   \n",
       "18  medext_v3  2020-11-05  2020-11-05 15:04:55        None          None   \n",
       "19  medext_v3  2020-11-05  2020-11-05 15:04:55        None          None   \n",
       "20  medext_v3  2020-11-05  2020-11-05 15:04:55        None          None   \n",
       "21  medext_v3  2020-11-05  2020-11-05 15:04:55        None          None   \n",
       "\n",
       "                                       term_modifiers validation_level_id  \n",
       "0   section='head',score='0.9963575005531311',snip...           automated  \n",
       "1           section='head',score='0.9664367139339447'           automated  \n",
       "2   section='head',score='0.9969384670257568',ATC_...           automated  \n",
       "3   section='head',score='0.9999349117279053',ATC_...           automated  \n",
       "4   section='head',score='0.9998010993003845',ATC_...           automated  \n",
       "5   section='head',score='0.9999445676803589',ENT/...           automated  \n",
       "6   section='head',score='0.9989744424819946',ATC_...           automated  \n",
       "7   section='head',score='0.8990024328231812',ATC_...           automated  \n",
       "8   section='head',score='0.9985721111297607',ATC_...           automated  \n",
       "9   section='head',score='0.9982656836509705',ATC_...           automated  \n",
       "10  section='head',score='0.9991045594215393',ATC_...           automated  \n",
       "11  section='head',score='0.9997856020927429',ENT/...           automated  \n",
       "12  section='head',score='0.9998668432235718',ATC_...           automated  \n",
       "13          section='head',score='0.9040422439575195'           automated  \n",
       "14  section='head',score='0.9988917708396912',ATC_...           automated  \n",
       "15  section='head',score='0.999586284160614',ENT/R...           automated  \n",
       "16  section='head',score='0.9997614026069641',ATC_...           automated  \n",
       "17  section='head',score='0.9998646974563599',snip...           automated  \n",
       "18  section='head',score='0.9986792206764221',ATC_...           automated  \n",
       "19  section='head',score='0.9984001517295837',ATC_...           automated  \n",
       "20  section='head',score='0.9977784752845764',ATC_...           automated  \n",
       "21  section='head',score='0.9606321454048157',ATC_...           automated  "
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pd.DataFrame.from_records(MedicationAnnotator.doc_to_omop(docs[1]))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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