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clinicalTrial_xml_singleFile.ipynb
66303 lines (66302 with data), 3.3 MB
{
"cells": [
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"import os\n",
"import re\n",
"import json\n",
"import sys\n",
"import pandas as pd\n",
"import numpy as np\n",
"import matplotlib.pyplot as plt\n",
"\n",
"import xml.etree.ElementTree as et\n",
"import io\n",
"import glob\n",
"from tqdm._tqdm_notebook import tqdm_notebook as tqdm\n",
"\n",
"#tqdm_notebook.pandas()"
]
},
{
"cell_type": "code",
"execution_count": 63,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"['MRI']\n"
]
}
],
"source": [
"xml_file = \"./new_data/combined_xml/NCT00058058.xml\"\n",
"tree = et.parse(xml_file)\n",
"root = tree.getroot()\n",
"col_names = ['nct_id', 'brief_title', 'official_title', 'overall_status', \n",
" 'start_date','completion_date', 'phase', 'study_type', \n",
" 'brief_summary', 'detailed_description', 'enrollment',\n",
" 'condition', 'intervention_name', 'eligibility']\n",
"\n",
"name1 = ['nct_id','brief_title', 'official_title', 'overall_status', \n",
" 'start_date','completion_date', 'phase', 'study_type', 'eligibility']\n",
"\n",
"name2 = ['brief_summary', 'detailed_description']\n",
" \n",
"name3 = ['enrollment', 'condition']\n",
"\n",
"df = pd.DataFrame(columns = col_names)\n",
"row = {name: ''for name in col_names} \n",
"\n",
"for d in tree.iter():\n",
" for txt in d.iter():\n",
" if d.tag in name1:\n",
" row[d.tag] = d.text\n",
" if d.tag in name2:\n",
" row[d.tag] = d.getchildren()[0].text\n",
" if d.tag in name3:\n",
" row[d.tag] = txt.text\n",
" if d.tag == \"intervention_name\":\n",
" intSearch = root.find('intervention_browse')\n",
" if intSearch:\n",
" row[d.tag]= [i.text for i in intSearch.findall('mesh_term')]\n",
" else:\n",
" row[d.tag] = [i.text for i in root.iter('intervention_name')]\n",
" if d.tag =='eligibility':\n",
" row[d.tag] = root.find('eligibility').find('criteria').find('textblock').text\n",
"df = df.append(pd.Series(row, index = col_names), ignore_index = True)\n",
"\n",
"for d in tree.iter():\n",
" if d.tag == \"intervention_name\":\n",
" intSearch = root.find('intervention_browse')\n",
" if intSearch:\n",
" print([i.text for i in intSearch.findall('mesh_term')])\n",
" else:\n",
" print([i.text for i in root.iter('intervention_name')])\n",
" #print(row[d.tag] == \"intervention_name\")\n",
"\n",
"# for fc in root:\n",
"# for sc in fc:\n",
"# if sc.tag in name1:\n",
"# print(sc.text) \n",
"# row[fc.tag] = fc.text\n",
"# if fc.tag in name2:\n",
"# row[fc.tag] = d.getchildren()[0].text\n",
"# if fc.tag in name3:\n",
"# row[fc.tag] = sc.text\n",
"# df = df.append(pd.Series(row, index = col_names), ignore_index = True)\n",
"\n",
"# for d in tree.iter():\n",
"# for txt in d.iter():\n",
"# if d.tag in name3:\n",
"# print(txt.text)"
]
},
{
"cell_type": "code",
"execution_count": 64,
"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>nct_id</th>\n",
" <th>brief_title</th>\n",
" <th>official_title</th>\n",
" <th>overall_status</th>\n",
" <th>start_date</th>\n",
" <th>completion_date</th>\n",
" <th>phase</th>\n",
" <th>study_type</th>\n",
" <th>brief_summary</th>\n",
" <th>detailed_description</th>\n",
" <th>enrollment</th>\n",
" <th>condition</th>\n",
" <th>intervention_name</th>\n",
" <th>eligibility</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>NCT00058058</td>\n",
" <td>Magnetic Resonance Imaging in Women Recently D...</td>\n",
" <td>MRI Evaluation Of The Contralateral Breast In ...</td>\n",
" <td>Completed</td>\n",
" <td>February 2003</td>\n",
" <td>August 2008</td>\n",
" <td>N/A</td>\n",
" <td>Interventional</td>\n",
" <td>\\n RATIONALE: Diagnostic procedures such ...</td>\n",
" <td>\\n OBJECTIVES:\\n\\n - Determine th...</td>\n",
" <td>1007</td>\n",
" <td>Contralateral Breast Cancer</td>\n",
" <td>MRI</td>\n",
" <td>\\n DISEASE CHARACTERISTICS:\\n\\n ...</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" nct_id brief_title \\\n",
"0 NCT00058058 Magnetic Resonance Imaging in Women Recently D... \n",
"\n",
" official_title overall_status \\\n",
"0 MRI Evaluation Of The Contralateral Breast In ... Completed \n",
"\n",
" start_date completion_date phase study_type \\\n",
"0 February 2003 August 2008 N/A Interventional \n",
"\n",
" brief_summary \\\n",
"0 \\n RATIONALE: Diagnostic procedures such ... \n",
"\n",
" detailed_description enrollment \\\n",
"0 \\n OBJECTIVES:\\n\\n - Determine th... 1007 \n",
"\n",
" condition intervention_name \\\n",
"0 Contralateral Breast Cancer MRI \n",
"\n",
" eligibility \n",
"0 \\n DISEASE CHARACTERISTICS:\\n\\n ... "
]
},
"execution_count": 64,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"#df.head()\n",
"df['intervention_name'] = df['intervention_name'].apply(', '.join)\n",
"df.head()"
]
},
{
"cell_type": "code",
"execution_count": 61,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'MRI'"
]
},
"execution_count": 61,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"df.intervention_name[0]"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"xml_file = \"./new_data/combined_xml/NCT00000500.xml\"\n",
"tree = et.parse(xml_file)\n",
"root = tree.getroot()\n",
"#res = []\n",
"#for t in root: \n",
"col_names = ['nct_id', 'brief_title', 'official_title', 'overall_status', \n",
" 'start_date','completion_date', 'phase', 'study_type', \n",
" 'brief_summary', 'detailed_description', \n",
" 'intervention','condition', 'enrollment']\n",
"\n",
"name1 = ['nct_id','brief_title', 'official_title', 'overall_status', \n",
" 'start_date','completion_date', 'phase', 'study_type']\n",
"\n",
"name2 = ['brief_summary', 'detailed_description']\n",
" \n",
"name3 = ['intervention','condition', 'enrollment']\n",
"\n",
"df = pd.DataFrame(columns = name1)\n",
"row = {name: ''for name in name1} \n",
"for d in tree.iter():\n",
" #for txt in d.iter():\n",
" if d.tag =='enrollment':\n",
" print(d)\n",
"\n",
"# if d.tag in name2:\n",
"# row[d.tag] = d.getchildren()[0].text\n",
"# if d.tag in name3:\n",
"# row[d.tag] = txt.text\n",
"# df = df.append(pd.Series(row, index = col_names), ignore_index = True)"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "92cff4a026564ddcb40868680e985e45",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"HBox(children=(IntProgress(value=0, max=61781), HTML(value='')))"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n"
]
}
],
"source": [
"filePath = glob.glob(\"./new_data/combined_xml/*.xml\")\n",
"col_names = ['nct_id', 'brief_title', 'official_title', 'overall_status', \n",
" 'start_date','completion_date', 'phase', 'study_type', \n",
" 'brief_summary', 'detailed_description', \n",
" 'intervention','condition', 'enrollment']\n",
"\n",
"name1 = ['nct_id','brief_title', 'official_title', 'overall_status', \n",
" 'start_date','completion_date', 'phase', 'study_type']\n",
"\n",
"name2 = ['brief_summary', 'detailed_description']\n",
"\n",
"name3 = ['intervention','condition', 'enrollment']\n",
"\n",
"df = pd.DataFrame(columns = col_names)\n",
"bad_file = []\n",
"\n",
"for files in tqdm(filePath):\n",
" try:\n",
" with open(files, 'r', encoding=\"utf-8\") as content:\n",
" tree = et.parse(content)\n",
" root = tree.getroot()\n",
"\n",
" row = {name: ''for name in col_names} \n",
"\n",
" for d in tree.iter():\n",
" for txt in d.iter():\n",
" if d.tag in name1:\n",
" row[d.tag] = d.text\n",
" if d.tag in name2:\n",
" row[d.tag] = d.getchildren()[0].text\n",
" if d.tag in name3:\n",
" row[d.tag] = txt.text\n",
" df = df.append(pd.Series(row, index = col_names), ignore_index = True)\n",
" except:\n",
" bad_file.append(files)\n"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"61781\n"
]
},
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
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" vertical-align: middle;\n",
" }\n",
"\n",
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" 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>nct_id</th>\n",
" <th>brief_title</th>\n",
" <th>official_title</th>\n",
" <th>overall_status</th>\n",
" <th>start_date</th>\n",
" <th>completion_date</th>\n",
" <th>phase</th>\n",
" <th>study_type</th>\n",
" <th>brief_summary</th>\n",
" <th>detailed_description</th>\n",
" <th>intervention</th>\n",
" <th>condition</th>\n",
" <th>enrollment</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>NCT00391586</td>\n",
" <td>Erlotinib and Standard Platinum-Based Chemothe...</td>\n",
" <td>INST 0601C: A Non-Randomized Phase II Protocol...</td>\n",
" <td>Terminated</td>\n",
" <td>July 2006</td>\n",
" <td>May 2012</td>\n",
" <td>Phase 2</td>\n",
" <td>Interventional</td>\n",
" <td>\\n This study was conducted to compare th...</td>\n",
" <td>\\n To compare the activities (the progres...</td>\n",
" <td>gemcitabine + platinum</td>\n",
" <td>Carcinoma, Non-Small-Cell Lung</td>\n",
" <td>45</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>NCT00058058</td>\n",
" <td>Magnetic Resonance Imaging in Women Recently D...</td>\n",
" <td>MRI Evaluation Of The Contralateral Breast In ...</td>\n",
" <td>Completed</td>\n",
" <td>February 2003</td>\n",
" <td>August 2008</td>\n",
" <td>N/A</td>\n",
" <td>Interventional</td>\n",
" <td>\\n RATIONALE: Diagnostic procedures such ...</td>\n",
" <td>\\n OBJECTIVES:\\n\\n - Determine th...</td>\n",
" <td>magnetic resonance imaging</td>\n",
" <td>Contralateral Breast Cancer</td>\n",
" <td>1007</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>NCT00038974</td>\n",
" <td>Hepatitis C Antiviral Resistance in African-Am...</td>\n",
" <td>Study of Viral Resistance to Antiviral Therapy...</td>\n",
" <td>Completed</td>\n",
" <td>August 2002</td>\n",
" <td>November 2005</td>\n",
" <td>Phase 3</td>\n",
" <td>Interventional</td>\n",
" <td>\\n This study is designed to test the hyp...</td>\n",
" <td></td>\n",
" <td>Interferon and rivavirin</td>\n",
" <td>Hepatitis C</td>\n",
" <td>401</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>NCT01473303</td>\n",
" <td>Combination Chemotherapy With or Without Ganit...</td>\n",
" <td>Phase IB/Randomized Phase II Study of Folfirin...</td>\n",
" <td>Withdrawn</td>\n",
" <td>August 2012</td>\n",
" <td></td>\n",
" <td>Phase 1/Phase 2</td>\n",
" <td>Interventional</td>\n",
" <td>\\n RATIONALE: Drugs used in chemotherapy,...</td>\n",
" <td>\\n OBJECTIVES:\\n\\n Primary\\n\\n ...</td>\n",
" <td>Arm II</td>\n",
" <td>Pancreatic Cancer</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>NCT02528643</td>\n",
" <td>A Study to Assess the Efficacy and Safety of E...</td>\n",
" <td>A Phase 2, Randomized, Double-Blind, Placebo-C...</td>\n",
" <td>Active, not recruiting</td>\n",
" <td>November 9, 2015</td>\n",
" <td>May 2019</td>\n",
" <td>Phase 2</td>\n",
" <td>Interventional</td>\n",
" <td>\\n The purpose of the study was to evalua...</td>\n",
" <td></td>\n",
" <td>Placebo</td>\n",
" <td>Advanced Hepatocellular Carcinoma</td>\n",
" <td>165</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" nct_id brief_title \\\n",
"0 NCT00391586 Erlotinib and Standard Platinum-Based Chemothe... \n",
"1 NCT00058058 Magnetic Resonance Imaging in Women Recently D... \n",
"2 NCT00038974 Hepatitis C Antiviral Resistance in African-Am... \n",
"3 NCT01473303 Combination Chemotherapy With or Without Ganit... \n",
"4 NCT02528643 A Study to Assess the Efficacy and Safety of E... \n",
"\n",
" official_title overall_status \\\n",
"0 INST 0601C: A Non-Randomized Phase II Protocol... Terminated \n",
"1 MRI Evaluation Of The Contralateral Breast In ... Completed \n",
"2 Study of Viral Resistance to Antiviral Therapy... Completed \n",
"3 Phase IB/Randomized Phase II Study of Folfirin... Withdrawn \n",
"4 A Phase 2, Randomized, Double-Blind, Placebo-C... Active, not recruiting \n",
"\n",
" start_date completion_date phase study_type \\\n",
"0 July 2006 May 2012 Phase 2 Interventional \n",
"1 February 2003 August 2008 N/A Interventional \n",
"2 August 2002 November 2005 Phase 3 Interventional \n",
"3 August 2012 Phase 1/Phase 2 Interventional \n",
"4 November 9, 2015 May 2019 Phase 2 Interventional \n",
"\n",
" brief_summary \\\n",
"0 \\n This study was conducted to compare th... \n",
"1 \\n RATIONALE: Diagnostic procedures such ... \n",
"2 \\n This study is designed to test the hyp... \n",
"3 \\n RATIONALE: Drugs used in chemotherapy,... \n",
"4 \\n The purpose of the study was to evalua... \n",
"\n",
" detailed_description \\\n",
"0 \\n To compare the activities (the progres... \n",
"1 \\n OBJECTIVES:\\n\\n - Determine th... \n",
"2 \n",
"3 \\n OBJECTIVES:\\n\\n Primary\\n\\n ... \n",
"4 \n",
"\n",
" intervention condition enrollment \n",
"0 gemcitabine + platinum Carcinoma, Non-Small-Cell Lung 45 \n",
"1 magnetic resonance imaging Contralateral Breast Cancer 1007 \n",
"2 Interferon and rivavirin Hepatitis C 401 \n",
"3 Arm II Pancreatic Cancer 0 \n",
"4 Placebo Advanced Hepatocellular Carcinoma 165 "
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"print(len(df))\n",
"df.head()"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"df.to_csv('cancerTrials.csv', index=False)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"[]"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"bad_file"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
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" vertical-align: top;\n",
" }\n",
"\n",
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"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>nct_id</th>\n",
" <th>brief_title</th>\n",
" <th>official_title</th>\n",
" <th>overall_status</th>\n",
" <th>start_date</th>\n",
" <th>completion_date</th>\n",
" <th>phase</th>\n",
" <th>study_type</th>\n",
" <th>brief_summary</th>\n",
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" <th>intervention</th>\n",
" <th>condition</th>\n",
" <th>enrollment</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>NCT01473303</td>\n",
" <td>Combination Chemotherapy With or Without Ganit...</td>\n",
" <td>Phase IB/Randomized Phase II Study of Folfirin...</td>\n",
" <td>Withdrawn</td>\n",
" <td>August 2012</td>\n",
" <td></td>\n",
" <td>Phase 1/Phase 2</td>\n",
" <td>Interventional</td>\n",
" <td>\\n RATIONALE: Drugs used in chemotherapy,...</td>\n",
" <td>\\n OBJECTIVES:\\n\\n Primary\\n\\n ...</td>\n",
" <td>Arm II</td>\n",
" <td>Pancreatic Cancer</td>\n",
" <td>0</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" nct_id brief_title \\\n",
"0 NCT01473303 Combination Chemotherapy With or Without Ganit... \n",
"\n",
" official_title overall_status \\\n",
"0 Phase IB/Randomized Phase II Study of Folfirin... Withdrawn \n",
"\n",
" start_date completion_date phase study_type \\\n",
"0 August 2012 Phase 1/Phase 2 Interventional \n",
"\n",
" brief_summary \\\n",
"0 \\n RATIONALE: Drugs used in chemotherapy,... \n",
"\n",
" detailed_description intervention \\\n",
"0 \\n OBJECTIVES:\\n\\n Primary\\n\\n ... Arm II \n",
"\n",
" condition enrollment \n",
"0 Pancreatic Cancer 0 "
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"df.tail()"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"./new_data/combined_xml/NCT00391586.xml\n",
"./new_data/combined_xml/NCT00058058.xml\n",
"./new_data/combined_xml/NCT00038974.xml\n",
"./new_data/combined_xml/NCT01473303.xml\n",
"./new_data/combined_xml/NCT02528643.xml\n",
"./new_data/combined_xml/NCT01435356.xml\n",
"./new_data/combined_xml/NCT01837862.xml\n",
"./new_data/combined_xml/NCT02181140.xml\n",
"./new_data/combined_xml/NCT01902173.xml\n",
"./new_data/combined_xml/NCT02568267.xml\n",
"./new_data/combined_xml/NCT02840162.xml\n",
"./new_data/combined_xml/NCT03180177.xml\n",
"./new_data/combined_xml/NCT03857737.xml\n",
"./new_data/combined_xml/NCT03228043.xml\n",
"./new_data/combined_xml/NCT00036959.xml\n",
"./new_data/combined_xml/NCT02518958.xml\n",
"./new_data/combined_xml/NCT02759016.xml\n",
"./new_data/combined_xml/NCT01794520.xml\n",
"./new_data/combined_xml/NCT02386683.xml\n",
"./new_data/combined_xml/NCT00335556.xml\n",
"./new_data/combined_xml/NCT00277017.xml\n",
"./new_data/combined_xml/NCT03102606.xml\n",
"./new_data/combined_xml/NCT00004055.xml\n",
"./new_data/combined_xml/NCT00348595.xml\n",
"./new_data/combined_xml/NCT01967927.xml\n",
"./new_data/combined_xml/NCT03853551.xml\n",
"./new_data/combined_xml/NCT03745716.xml\n",
"./new_data/combined_xml/NCT02640235.xml\n",
"./new_data/combined_xml/NCT01376752.xml\n",
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"./new_data/combined_xml/NCT00191269.xml\n",
"./new_data/combined_xml/NCT01364415.xml\n",
"./new_data/combined_xml/NCT02048371.xml\n",
"./new_data/combined_xml/NCT02375048.xml\n",
"./new_data/combined_xml/NCT00520325.xml\n",
"./new_data/combined_xml/NCT03740893.xml\n",
"./new_data/combined_xml/NCT00104702.xml\n",
"./new_data/combined_xml/NCT01155102.xml\n",
"./new_data/combined_xml/NCT00747474.xml\n",
"./new_data/combined_xml/NCT00561379.xml\n",
"./new_data/combined_xml/NCT03526562.xml\n",
"./new_data/combined_xml/NCT02323568.xml\n",
"./new_data/combined_xml/NCT01083550.xml\n",
"./new_data/combined_xml/NCT02061085.xml\n",
"./new_data/combined_xml/NCT01710605.xml\n",
"./new_data/combined_xml/NCT01305941.xml\n",
"./new_data/combined_xml/NCT01001221.xml\n",
"./new_data/combined_xml/NCT00474760.xml\n",
"./new_data/combined_xml/NCT00809458.xml\n",
"./new_data/combined_xml/NCT03415802.xml\n",
"./new_data/combined_xml/NCT00019747.xml\n",
"./new_data/combined_xml/NCT01878188.xml\n",
"./new_data/combined_xml/NCT00140140.xml\n",
"./new_data/combined_xml/NCT02626195.xml\n",
"./new_data/combined_xml/NCT02611739.xml\n",
"./new_data/combined_xml/NCT00109226.xml\n",
"./new_data/combined_xml/NCT00781547.xml\n",
"./new_data/combined_xml/NCT03252912.xml\n",
"./new_data/combined_xml/NCT03907657.xml\n",
"./new_data/combined_xml/NCT02099058.xml\n",
"./new_data/combined_xml/NCT02013375.xml\n",
"./new_data/combined_xml/NCT00982319.xml\n",
"./new_data/combined_xml/NCT01814046.xml\n",
"./new_data/combined_xml/NCT00004070.xml\n",
"./new_data/combined_xml/NCT00096512.xml\n",
"./new_data/combined_xml/NCT03575884.xml\n",
"./new_data/combined_xml/NCT02608268.xml\n",
"./new_data/combined_xml/NCT01899404.xml\n",
"./new_data/combined_xml/NCT01694277.xml\n",
"./new_data/combined_xml/NCT00476177.xml\n",
"./new_data/combined_xml/NCT00083889.xml\n",
"./new_data/combined_xml/NCT03399487.xml\n",
"./new_data/combined_xml/NCT00923299.xml\n",
"./new_data/combined_xml/NCT00113256.xml\n",
"./new_data/combined_xml/NCT01018758.xml\n",
"./new_data/combined_xml/NCT01779843.xml\n",
"./new_data/combined_xml/NCT02560636.xml\n",
"./new_data/combined_xml/NCT00381940.xml\n",
"./new_data/combined_xml/NCT01860937.xml\n",
"./new_data/combined_xml/NCT03398941.xml\n",
"./new_data/combined_xml/NCT01423539.xml\n",
"./new_data/combined_xml/NCT01152645.xml\n",
"./new_data/combined_xml/NCT02405910.xml\n",
"./new_data/combined_xml/NCT02576054.xml\n",
"./new_data/combined_xml/NCT01785420.xml\n",
"./new_data/combined_xml/NCT03719716.xml\n",
"./new_data/combined_xml/NCT00027859.xml\n",
"./new_data/combined_xml/NCT03903419.xml\n",
"./new_data/combined_xml/NCT03761875.xml\n",
"./new_data/combined_xml/NCT00573755.xml\n",
"./new_data/combined_xml/NCT01542879.xml\n",
"./new_data/combined_xml/NCT02448810.xml\n",
"./new_data/combined_xml/NCT02108769.xml\n",
"./new_data/combined_xml/NCT01574313.xml\n",
"./new_data/combined_xml/NCT03533621.xml\n",
"./new_data/combined_xml/NCT01958502.xml\n",
"./new_data/combined_xml/NCT02666599.xml\n",
"./new_data/combined_xml/NCT00004058.xml\n",
"./new_data/combined_xml/NCT00064974.xml\n",
"./new_data/combined_xml/NCT00024388.xml\n",
"./new_data/combined_xml/NCT01367652.xml\n",
"./new_data/combined_xml/NCT02844309.xml\n",
"./new_data/combined_xml/NCT00920790.xml\n",
"./new_data/combined_xml/NCT01377441.xml\n",
"./new_data/combined_xml/NCT00003737.xml\n",
"./new_data/combined_xml/NCT01657214.xml\n",
"./new_data/combined_xml/NCT00804154.xml\n",
"./new_data/combined_xml/NCT01273155.xml\n",
"./new_data/combined_xml/NCT01666977.xml\n",
"./new_data/combined_xml/NCT00896350.xml\n",
"./new_data/combined_xml/NCT00427310.xml\n",
"./new_data/combined_xml/NCT02429544.xml\n",
"./new_data/combined_xml/NCT02116231.xml\n",
"./new_data/combined_xml/NCT02888717.xml\n",
"./new_data/combined_xml/NCT02213497.xml\n",
"./new_data/combined_xml/NCT03449199.xml\n",
"./new_data/combined_xml/NCT02901899.xml\n",
"./new_data/combined_xml/NCT03013712.xml\n",
"./new_data/combined_xml/NCT00781209.xml\n",
"./new_data/combined_xml/NCT00253812.xml\n",
"./new_data/combined_xml/NCT02493972.xml\n",
"./new_data/combined_xml/NCT00158041.xml\n",
"./new_data/combined_xml/NCT00696007.xml\n",
"./new_data/combined_xml/NCT02049047.xml\n",
"./new_data/combined_xml/NCT01123902.xml\n",
"./new_data/combined_xml/NCT03808558.xml\n",
"./new_data/combined_xml/NCT00115141.xml\n",
"./new_data/combined_xml/NCT00031785.xml\n",
"./new_data/combined_xml/NCT02227732.xml\n",
"./new_data/combined_xml/NCT00041262.xml\n",
"./new_data/combined_xml/NCT02681302.xml\n",
"./new_data/combined_xml/NCT03746574.xml\n",
"./new_data/combined_xml/NCT01475019.xml\n",
"./new_data/combined_xml/NCT03501693.xml\n",
"./new_data/combined_xml/NCT01841047.xml\n",
"./new_data/combined_xml/NCT00902525.xml\n",
"./new_data/combined_xml/NCT00324324.xml\n",
"./new_data/combined_xml/NCT03571360.xml\n",
"./new_data/combined_xml/NCT03017560.xml\n",
"./new_data/combined_xml/NCT00975975.xml\n",
"./new_data/combined_xml/NCT03726294.xml\n",
"./new_data/combined_xml/NCT00756223.xml\n",
"./new_data/combined_xml/NCT01905163.xml\n",
"./new_data/combined_xml/NCT03435250.xml\n",
"./new_data/combined_xml/NCT01519869.xml\n",
"./new_data/combined_xml/NCT00740441.xml\n",
"./new_data/combined_xml/NCT02391480.xml\n",
"./new_data/combined_xml/NCT02878382.xml\n",
"./new_data/combined_xml/NCT00017030.xml\n",
"./new_data/combined_xml/NCT03028948.xml\n",
"./new_data/combined_xml/NCT02806648.xml\n",
"./new_data/combined_xml/NCT02220049.xml\n",
"./new_data/combined_xml/NCT03682536.xml\n",
"./new_data/combined_xml/NCT00394381.xml\n",
"./new_data/combined_xml/NCT00222027.xml\n",
"./new_data/combined_xml/NCT01554969.xml\n",
"./new_data/combined_xml/NCT02916329.xml\n",
"./new_data/combined_xml/NCT00003045.xml\n",
"./new_data/combined_xml/NCT00936858.xml\n",
"./new_data/combined_xml/NCT02611063.xml\n",
"./new_data/combined_xml/NCT01897415.xml\n",
"./new_data/combined_xml/NCT03139851.xml\n",
"./new_data/combined_xml/NCT01429766.xml\n",
"./new_data/combined_xml/NCT03003273.xml\n",
"./new_data/combined_xml/NCT03900104.xml\n",
"./new_data/combined_xml/NCT01573468.xml\n",
"./new_data/combined_xml/NCT01685346.xml\n",
"./new_data/combined_xml/NCT02106988.xml\n",
"./new_data/combined_xml/NCT02936947.xml\n",
"./new_data/combined_xml/NCT03160924.xml\n",
"./new_data/combined_xml/NCT03467516.xml\n",
"./new_data/combined_xml/NCT03909646.xml\n",
"./new_data/combined_xml/NCT03854227.xml\n",
"./new_data/combined_xml/NCT03420885.xml\n",
"./new_data/combined_xml/NCT01091168.xml\n",
"./new_data/combined_xml/NCT00107237.xml\n",
"./new_data/combined_xml/NCT00003723.xml\n",
"./new_data/combined_xml/NCT01985763.xml\n",
"./new_data/combined_xml/NCT00623870.xml\n",
"./new_data/combined_xml/NCT00654420.xml\n",
"./new_data/combined_xml/NCT02820857.xml\n",
"./new_data/combined_xml/NCT02750995.xml\n",
"./new_data/combined_xml/NCT03435536.xml\n",
"./new_data/combined_xml/NCT03876938.xml\n",
"./new_data/combined_xml/NCT01913067.xml\n",
"./new_data/combined_xml/NCT00103051.xml\n",
"./new_data/combined_xml/NCT00954005.xml\n",
"./new_data/combined_xml/NCT02662933.xml\n",
"./new_data/combined_xml/NCT00365378.xml\n",
"./new_data/combined_xml/NCT00741039.xml\n",
"./new_data/combined_xml/NCT03396978.xml\n",
"./new_data/combined_xml/NCT00944216.xml\n",
"./new_data/combined_xml/NCT01198158.xml\n",
"./new_data/combined_xml/NCT03175497.xml\n"
]
}
],
"source": [
"filePath = glob.glob(\"./new_data/combined_xml/NCT*.xml\")\n",
"for files in filePath:\n",
" print(files)\n",
" #with open(files, 'r', encoding=\"utf-8\") as content:"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"<Element 'required_header' at 0x12353c818>\n",
"<Element 'id_info' at 0x1238b7688>\n",
"<Element 'brief_title' at 0x1238b7cc8>\n",
"<Element 'sponsors' at 0x1238b7ea8>\n",
"<Element 'source' at 0x1238b7ae8>\n",
"<Element 'brief_summary' at 0x1238b7818>\n",
"<Element 'detailed_description' at 0x1238b77c8>\n",
"<Element 'overall_status' at 0x1238b7368>\n",
"<Element 'start_date' at 0x1238b7638>\n",
"<Element 'completion_date' at 0x1238b7548>\n",
"<Element 'primary_completion_date' at 0x11f2f7688>\n",
"<Element 'phase' at 0x11f2f7958>\n",
"<Element 'study_type' at 0x11f2f7548>\n",
"<Element 'has_expanded_access' at 0x12398dd68>\n",
"<Element 'study_design_info' at 0x12398dd18>\n",
"<Element 'condition' at 0x12398d4f8>\n",
"<Element 'condition' at 0x12393b458>\n",
"<Element 'condition' at 0x12393b548>\n",
"<Element 'condition' at 0x12393b6d8>\n",
"<Element 'intervention' at 0x12393b8b8>\n",
"<Element 'intervention' at 0x12393be58>\n",
"<Element 'eligibility' at 0x12393b818>\n",
"<Element 'reference' at 0x12393b2c8>\n",
"<Element 'reference' at 0x12158cef8>\n",
"<Element 'reference' at 0x122c9d9f8>\n",
"<Element 'reference' at 0x122c9dbd8>\n",
"<Element 'reference' at 0x122c9dc28>\n",
"<Element 'reference' at 0x122c9da98>\n",
"<Element 'reference' at 0x122cb0f48>\n",
"<Element 'reference' at 0x122cb0cc8>\n",
"<Element 'reference' at 0x122cb0228>\n",
"<Element 'reference' at 0x122cb06d8>\n",
"<Element 'reference' at 0x122cb0d18>\n",
"<Element 'reference' at 0x123814db8>\n",
"<Element 'reference' at 0x123814868>\n",
"<Element 'reference' at 0x123814638>\n",
"<Element 'reference' at 0x123814368>\n",
"<Element 'reference' at 0x123814e58>\n",
"<Element 'reference' at 0x123814c28>\n",
"<Element 'reference' at 0x123814b38>\n",
"<Element 'reference' at 0x123814598>\n",
"<Element 'reference' at 0x1238145e8>\n",
"<Element 'reference' at 0x1238147c8>\n",
"<Element 'reference' at 0x123814778>\n",
"<Element 'reference' at 0x12348bae8>\n",
"<Element 'reference' at 0x12348b688>\n",
"<Element 'reference' at 0x1223a4228>\n",
"<Element 'reference' at 0x12314f3b8>\n",
"<Element 'reference' at 0x12314f368>\n",
"<Element 'reference' at 0x12314f6d8>\n",
"<Element 'reference' at 0x12314f318>\n",
"<Element 'reference' at 0x12066bf48>\n",
"<Element 'reference' at 0x122796368>\n",
"<Element 'reference' at 0x121dd5ef8>\n",
"<Element 'reference' at 0x123bf9a98>\n",
"<Element 'reference' at 0x123bf9098>\n",
"<Element 'reference' at 0x123bf9b38>\n",
"<Element 'reference' at 0x123bf9818>\n",
"<Element 'reference' at 0x123bf9458>\n",
"<Element 'reference' at 0x123bf9958>\n",
"<Element 'reference' at 0x123bf99a8>\n",
"<Element 'reference' at 0x123bf98b8>\n",
"<Element 'reference' at 0x123bf93b8>\n",
"<Element 'reference' at 0x123bf9048>\n",
"<Element 'reference' at 0x123bf99f8>\n",
"<Element 'reference' at 0x123bf94a8>\n",
"<Element 'reference' at 0x123bf9ef8>\n",
"<Element 'reference' at 0x123bf9778>\n",
"<Element 'reference' at 0x122edf188>\n",
"<Element 'reference' at 0x122edf318>\n",
"<Element 'reference' at 0x122604d68>\n",
"<Element 'reference' at 0x11f74ae08>\n",
"<Element 'reference' at 0x123263d68>\n",
"<Element 'reference' at 0x123263f98>\n",
"<Element 'reference' at 0x123263c28>\n",
"<Element 'reference' at 0x123263278>\n",
"<Element 'reference' at 0x1238ec728>\n",
"<Element 'reference' at 0x1238ec638>\n",
"<Element 'reference' at 0x1238ec1d8>\n",
"<Element 'reference' at 0x1238ec3b8>\n",
"<Element 'reference' at 0x1238ec5e8>\n",
"<Element 'reference' at 0x1238eca98>\n",
"<Element 'reference' at 0x1238ec2c8>\n",
"<Element 'reference' at 0x1238ecb88>\n",
"<Element 'reference' at 0x1238ec188>\n",
"<Element 'reference' at 0x1238ec0e8>\n",
"<Element 'reference' at 0x1238ec818>\n",
"<Element 'reference' at 0x1238ec9f8>\n",
"<Element 'reference' at 0x1238ecb38>\n",
"<Element 'reference' at 0x1238ec138>\n",
"<Element 'reference' at 0x121d079f8>\n",
"<Element 'reference' at 0x123c05c78>\n",
"<Element 'reference' at 0x123c05598>\n",
"<Element 'reference' at 0x123c056d8>\n",
"<Element 'reference' at 0x123c05e58>\n",
"<Element 'verification_date' at 0x123c055e8>\n",
"<Element 'study_first_submitted' at 0x123c05d18>\n",
"<Element 'study_first_submitted_qc' at 0x123c057c8>\n",
"<Element 'study_first_posted' at 0x123c05278>\n",
"<Element 'last_update_submitted' at 0x123c05818>\n",
"<Element 'last_update_submitted_qc' at 0x123c054f8>\n",
"<Element 'last_update_posted' at 0x123c05728>\n",
"<Element 'responsible_party' at 0x123c050e8>\n",
"<Element 'condition_browse' at 0x123c05ae8>\n",
"<Element 'intervention_browse' at 0x12353cc78>\n"
]
}
],
"source": [
"xml_file = \"./new_data/combined_xml/NCT00000500.xml\"\n",
"tree = et.parse(xml_file)\n",
"root = tree.getroot()\n",
"\n",
"#res = []\n",
"#for t in root: \n",
"#col_names = \n",
"# name1 = ['nct_id', 'official_title', 'overall_status', \n",
"# 'start_date','completion_date', 'phase', 'study_type']\n",
"name2 = ['brief_summary', 'detailed_description', 'intervention', \n",
" 'condition', 'enrollment', 'eligibility']\n",
"df = pd.DataFrame(columns = name2)\n",
"row = {name: ''for name in name2} \n",
"for attribute in root:\n",
" print(attribute)\n",
"# for d in tree.iter():\n",
"# if d.tag =='condition':\n",
"# print([txt.text for txt in d.iter()])\n",
" \n",
"# if d.tag =='brief_summary':\n",
"# print(d.getchildren()[0].text)\n",
" \n",
"# df = df.append(pd.Series(row), ignore_index = True)\n",
"# df\n",
"#return df \n",
"# elif d.tag in name2:\n",
"# print d.attrib.values()[0]\n",
"\n",
"# for child in root:\n",
"# #print(child.tag, child.attrib, child.text)\n",
"# if child.tag == 'id_info':\n",
"# for c in child:\n",
"# print(c.tag, c.attrib, c.text)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": 11,
"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>brief_summary</th>\n",
" <th>detailed_description</th>\n",
" <th>intervention</th>\n",
" <th>condition</th>\n",
" <th>enrollment</th>\n",
" <th>eligibility</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
"Empty DataFrame\n",
"Columns: [brief_summary, detailed_description, intervention, condition, enrollment, eligibility]\n",
"Index: []"
]
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"df"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [],
"source": [
"xml_file = \"./data/search_result/NCT00000479.xml\""
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [],
"source": [
"def parse_XML(xml_file): \n",
" \"\"\"Parse the input XML file and store the result \n",
" in a pandas DataFrame with the given columns\"\"\"\n",
" tree = et.parse(xml_file)\n",
" root = tree.getroot()\n",
" text = {}\n",
" df_cols = ['eligibility', 'intervention_name', 'condition', 'enrollment']\n",
" \n",
" df = pd.DataFrame(columns = df_cols)\n",
" \n",
" try:\n",
" for tag in tags:\n",
" if tag == \"eligibility\" :\n",
" text[tag]= root.find('eligibility').find('criteria').find('textblock').text\n",
" if tag == \"intervention_name\":\n",
" intBrowse = root.find('intervention_browse')\n",
" if intBrowse:\n",
" text[tag]= [i.text for i in intBrowse.findall('mesh_term') ]\n",
" else:\n",
" text[tag] = [i.text for i in root.iter('intervention_name') ]\n",
" if tag == \"condition\" :\n",
" text[tag]= [c.text for c in root.findall('condition') ]\n",
" if tag == \"enrollment\":\n",
" text[tag]= root.find('enrollment').text\n",
" except:\n",
" print (\"no eligibility criteria\")\n",
"\n",
" df = df.append(pd.Series(text, index = df_cols), ignore_index = True)\n",
"\n",
" return df"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"no eligibility criteria\n"
]
},
{
"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>eligibility</th>\n",
" <th>intervention_name</th>\n",
" <th>condition</th>\n",
" <th>enrollment</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" eligibility intervention_name condition enrollment\n",
"0 NaN NaN NaN NaN"
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"parse_XML(xml_file)"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [],
"source": [
"def parse_XML(xml_file): \n",
" \"\"\"Parse the input XML file and store the result \n",
" in a pandas DataFrame with the given columns\"\"\"\n",
" tree = et.parse(xml_file)\n",
" root = tree.getroot()\n",
" \n",
"# df_cols = ['clinical_study', 'nct_id', 'official_title',\n",
"# 'brief_summary', 'detailed_description', 'overall_status', \n",
"# 'start_date','completion_date', 'phase', 'study_type', \n",
"# 'study_design_info','eligibility','intervention', 'condition', \n",
"# 'enrollment']\n",
"\n",
" df_cols = ['clinical_study', 'nct_id', 'official_title']\n",
" \n",
" df = pd.DataFrame(columns = df_cols)\n",
"\n",
" for node in root: \n",
" clinical_study = node.attrib.get('rank')\n",
" nct_id = node.find('nct_id')\n",
" official_title = node.find('official_title')\n",
"# brief_summary = node.find('brief_summary')\n",
"# detailed_description = node.find('detailed_description')\n",
"# overall_status = node.find('overall_status')\n",
"# start_date = node.attrib.get('start_date')\n",
"# completion_date = node.attrib.get('completion_date')\n",
"# phase = node.attrib.get('phase')\n",
"# study_type = node.attrib.get('study_type')\n",
"# study_design_info = node.attrib.get('study_design_info')\n",
"# #eligibility = node.find('eligibility').find('criteria').find('textblock').text\n",
"# intervention = node.find('intervention_browse')\n",
"# condition = node.findall('condition')\n",
"# #enrollment = node.find('enrollment').text\n",
"\n",
" df = df.append(pd.Series([clinical_study, nct_id, official_title], index = df_cols), ignore_index = True)\n",
"\n",
" return df"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
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" <td>None</td>\n",
" <td>None</td>\n",
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" <th>19</th>\n",
" <td>None</td>\n",
" <td>None</td>\n",
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" <th>20</th>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
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" <th>21</th>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
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" <tr>\n",
" <th>22</th>\n",
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" <th>25</th>\n",
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" <th>26</th>\n",
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" <td>None</td>\n",
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" <td>None</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
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" <th>28</th>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
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" <th>29</th>\n",
" <td>None</td>\n",
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" <th>107</th>\n",
" <td>None</td>\n",
" <td>None</td>\n",
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" <tr>\n",
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" <th>109</th>\n",
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" <th>110</th>\n",
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" <th>116</th>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>117</th>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>118</th>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>119</th>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>120</th>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>121</th>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>122</th>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
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" <tr>\n",
" <th>123</th>\n",
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" <tr>\n",
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" <td>None</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>125</th>\n",
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" <tr>\n",
" <th>127</th>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>128</th>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>129</th>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>130</th>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>131</th>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>132</th>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>133</th>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>134</th>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>135 rows × 3 columns</p>\n",
"</div>"
],
"text/plain": [
" clinical_study nct_id official_title\n",
"0 None None None\n",
"1 None [] None\n",
"2 None None None\n",
"3 None None None\n",
"4 None None None\n",
"5 None None None\n",
"6 None None None\n",
"7 None None None\n",
"8 None None None\n",
"9 None None None\n",
"10 None None None\n",
"11 None None None\n",
"12 None None None\n",
"13 None None None\n",
"14 None None None\n",
"15 None None None\n",
"16 None None None\n",
"17 None None None\n",
"18 None None None\n",
"19 None None None\n",
"20 None None None\n",
"21 None None None\n",
"22 None None None\n",
"23 None None None\n",
"24 None None None\n",
"25 None None None\n",
"26 None None None\n",
"27 None None None\n",
"28 None None None\n",
"29 None None None\n",
".. ... ... ...\n",
"105 None None None\n",
"106 None None None\n",
"107 None None None\n",
"108 None None None\n",
"109 None None None\n",
"110 None None None\n",
"111 None None None\n",
"112 None None None\n",
"113 None None None\n",
"114 None None None\n",
"115 None None None\n",
"116 None None None\n",
"117 None None None\n",
"118 None None None\n",
"119 None None None\n",
"120 None None None\n",
"121 None None None\n",
"122 None None None\n",
"123 None None None\n",
"124 None None None\n",
"125 None None None\n",
"126 None None None\n",
"127 None None None\n",
"128 None None None\n",
"129 None None None\n",
"130 None None None\n",
"131 None None None\n",
"132 None None None\n",
"133 None None None\n",
"134 None None None\n",
"\n",
"[135 rows x 3 columns]"
]
},
"execution_count": 16,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"file_path = \"./data/search_result/NCT00000479.xml\"\n",
"\n",
"parse_XML(file_path)"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"required_header {}\n",
"id_info {}\n",
"brief_title {}\n",
"sponsors {}\n",
"source {}\n",
"brief_summary {}\n",
"detailed_description {}\n",
"overall_status {}\n",
"start_date {}\n",
"completion_date {'type': 'Actual'}\n",
"primary_completion_date {'type': 'Actual'}\n",
"phase {}\n",
"study_type {}\n",
"has_expanded_access {}\n",
"study_design_info {}\n",
"condition {}\n",
"condition {}\n",
"condition {}\n",
"condition {}\n",
"intervention {}\n",
"intervention {}\n",
"eligibility {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"verification_date {}\n",
"study_first_submitted {}\n",
"study_first_submitted_qc {}\n",
"study_first_posted {'type': 'Estimate'}\n",
"last_update_submitted {}\n",
"last_update_submitted_qc {}\n",
"last_update_posted {'type': 'Estimate'}\n",
"responsible_party {}\n",
"condition_browse {}\n",
"intervention_browse {}\n"
]
}
],
"source": [
"for child in root:\n",
" print(child.tag, child.attrib)"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {},
"outputs": [],
"source": [
"from xmljson import badgerfish as bf\n",
"from xml.etree.ElementTree import fromstring"
]
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"{\r\n",
" \"clinical_study\": {\r\n",
" \"@rank\": 5313,\r\n",
" \"required_header\": {\r\n",
" \"download_date\": {\r\n",
" \"$\": \"ClinicalTrials.gov processed this data on April 29, 2019\"\r\n",
" },\r\n",
" \"link_text\": {\r\n",
" \"$\": \"Link to the current ClinicalTrials.gov record.\"\r\n",
" },\r\n",
" \"url\": {\r\n",
" \"$\": \"https://clinicaltrials.gov/show/NCT00000479\"\r\n",
" }\r\n",
" },\r\n",
" \"id_info\": {\r\n",
" \"org_study_id\": {\r\n",
" \"$\": 69\r\n",
" },\r\n",
" \"secondary_id\": [\r\n",
" {\r\n",
" \"$\": \"R01HL043851\"\r\n",
" },\r\n",
" {\r\n",
" \"$\": \"HL043851\"\r\n",
" },\r\n",
" {\r\n",
" \"$\": \"CA047988\"\r\n",
" }\r\n",
" ],\r\n",
" \"nct_id\": {\r\n",
" \"$\": \"NCT00000479\"\r\n",
" }\r\n",
" },\r\n",
" \"brief_title\": {\r\n",
" \"$\": \"Women's Health Study (WHS): A Randomized Trial of Low-dose Aspirin and Vitamin E in the Primary Prevention of Cardiovascular Disease and Cancer\"\r\n",
" },\r\n",
" \"acronym\": {\r\n",
" \"$\": \"WHS\"\r\n",
" },\r\n",
" \"official_title\": {\r\n",
" \"$\": \"Women's Health Study of Low-dose Aspirin and Vitamin E in Apparently Healthy Women\"\r\n",
" },\r\n",
" \"sponsors\": {\r\n",
" \"lead_sponsor\": {\r\n",
" \"agency\": {\r\n",
" \"$\": \"Brigham and Women's Hospital\"\r\n",
" },\r\n",
" \"agency_class\": {\r\n",
" \"$\": \"Other\"\r\n",
" }\r\n",
" },\r\n",
" \"collaborator\": [\r\n",
" {\r\n",
" \"agency\": {\r\n",
" \"$\": \"National Cancer Institute (NCI)\"\r\n",
" },\r\n",
" \"agency_class\": {\r\n",
" \"$\": \"NIH\"\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"agency\": {\r\n",
" \"$\": \"National Heart, Lung, and Blood Institute (NHLBI)\"\r\n",
" },\r\n",
" \"agency_class\": {\r\n",
" \"$\": \"NIH\"\r\n",
" }\r\n",
" }\r\n",
" ]\r\n",
" },\r\n",
" \"source\": {\r\n",
" \"$\": \"Brigham and Women's Hospital\"\r\n",
" },\r\n",
" \"oversight_info\": {\r\n",
" \"has_dmc\": {\r\n",
" \"$\": \"Yes\"\r\n",
" }\r\n",
" },\r\n",
" \"brief_summary\": {\r\n",
" \"textblock\": {\r\n",
" \"$\": \"The purpose of this study is to evaluate the effects of low-dose aspirin and vitamin E in\\n primary prevention of cardiovascular disease and cancer in apparently healthy women.\"\r\n",
" }\r\n",
" },\r\n",
" \"detailed_description\": {\r\n",
" \"textblock\": {\r\n",
" \"$\": \"BACKGROUND:\\n\\n Various doses of aspirin have been shown to be effective in preventing thrombosis or vascular\\n occlusion in several clinical conditions. Short-term studies have documented the efficacy of\\n aspirin in preventing occlusion of saphenous vein bypass grants, preventing myocardial\\n infarction in patients with unstable angina, preventing transient ischemic attacks and stroke\\n in men with cerebral vascular disease, preventing occlusion of injured coronary arteries\\n following transluminal angioplasty and aiding in reducing myocardial infarction and total\\n mortality in patients receiving fibrinolytic therapy. Additionally, aspirin has been\\n effective in the secondary prevention of myocardial infarction in subjects with known\\n coronary artery disease. The results of the Physicians' Health Study, a large-scale primary\\n prevention trial of aspirin in male physicians, have shown a decrease in myocardial\\n infarction, a non-significant increase in cerebral vascular events, and no difference in\\n overall mortality. However, few studies have addressed the efficacy of aspirin in vascular\\n diseases in women, and it is possible that the risk to benefit ratio may be different in\\n women. Specifically, there have been no large primary prevention trials in women, who are at\\n risk of coronary heart disease, especially after menopause.\\n\\n DESIGN NARRATIVE:\\n\\n The Women's Health Study (WHS) is a randomized, double-blind, placebo-controlled trial using\\n a 2x2 factorial design. The WHS is sponsored by both NHBLI (HL080467) and NCI (CA047988).\\n Approximately 1.75 million female health professionals were contacted by mail to determine if\\n they were suitable for inclusion in the study. A three-month run-in phase was performed to\\n screen out those with poor compliance. Randomization, which began in February 1993 and ended\\n in January 1996, was stratified on five-year age groups. A total of 39,876 participants were\\n randomly assigned to either Vitamin E (600 IU every other day) or placebo; and to aspirin\\n (100 mg every other day) or placebo. IN the 2x2 factorial design, women were randomly\\n assigned to active aspirin and placebo vitamin E (n=9,968), placebo aspirin and active\\n vitamin E (n=9,971), active aspirin and active vitamin E (n=9,966), or placebo aspirin and\\n placebo vitamin E (n=9,971). A description of the characteristics of women in these 4 groups\\n is provided in J Women's Health Gend Based Med 2000;9:19-27. In the main analyses, all women\\n on active aspirin (n=19,934) were compared to women on placebo aspirin (n=19,942); and all\\n women on active vitamin E (n=19,937) were compared to women on placebo aspirin (n=19,939).\\n\\n As part of the initial trial, pre-randomization blood samples from 28,345 participants were\\n frozen and stored for genetic analysis which has been supported by non-federal sources.\\n\\n The primary endpoint is the reduction of the risk of all important vascular events (a\\n combined endpoint of nonfatal myocardial infarction, nonfatal stroke, and total\\n cardiovascular death) and a decrease in the incidence of total malignant neoplasms of\\n epithelial cell origin. Secondary endpoints are the individual components of the combined\\n endpoints. Compliance is measured by replies to a questionnaire sent out every year. The\\n trial was completed in 2004 and results were published in 2005 (N Engl J Med\\n 2005;352:1293-304; JAMA 2005;294:47-55; JAMA 2005;294:56-65).\\n\\n Currently, women are being followed on an observational basis.\"\r\n",
" }\r\n",
" },\r\n",
" \"overall_status\": {\r\n",
" \"$\": \"Completed\"\r\n",
" },\r\n",
" \"start_date\": {\r\n",
" \"$\": \"September 1992\"\r\n",
" },\r\n",
" \"completion_date\": {\r\n",
" \"@type\": \"Actual\",\r\n",
" \"$\": \"February 2005\"\r\n",
" },\r\n",
" \"primary_completion_date\": {\r\n",
" \"@type\": \"Actual\",\r\n",
" \"$\": \"March 2004\"\r\n",
" },\r\n",
" \"phase\": {\r\n",
" \"$\": \"Phase 3\"\r\n",
" },\r\n",
" \"study_type\": {\r\n",
" \"$\": \"Interventional\"\r\n",
" },\r\n",
" \"has_expanded_access\": {\r\n",
" \"$\": \"No\"\r\n",
" },\r\n",
" \"study_design_info\": {\r\n",
" \"allocation\": {\r\n",
" \"$\": \"Randomized\"\r\n",
" },\r\n",
" \"intervention_model\": {\r\n",
" \"$\": \"Factorial Assignment\"\r\n",
" },\r\n",
" \"primary_purpose\": {\r\n",
" \"$\": \"Prevention\"\r\n",
" },\r\n",
" \"masking\": {\r\n",
" \"$\": \"Triple (Participant, Investigator, Outcomes Assessor)\"\r\n",
" }\r\n",
" },\r\n",
" \"primary_outcome\": [\r\n",
" {\r\n",
" \"measure\": {\r\n",
" \"$\": \"Number of Participants With Major Cardiovascular Events (a Combined Endpoint of Nonfatal Myocardial Infarction, Nonfatal Stroke, and Total Cardiovascular Death)\"\r\n",
" },\r\n",
" \"time_frame\": {\r\n",
" \"$\": \"Average follow-up 10.1 years\"\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"measure\": {\r\n",
" \"$\": \"Number of Participants With Cancer, Excluding Nonmelanoma Skin Cancer\"\r\n",
" },\r\n",
" \"time_frame\": {\r\n",
" \"$\": \"Average follow-up 10.1 years\"\r\n",
" }\r\n",
" }\r\n",
" ],\r\n",
" \"number_of_arms\": {\r\n",
" \"$\": 4\r\n",
" },\r\n",
" \"enrollment\": {\r\n",
" \"@type\": \"Actual\",\r\n",
" \"$\": 39876\r\n",
" },\r\n",
" \"condition\": [\r\n",
" {\r\n",
" \"$\": \"Cardiovascular Diseases\"\r\n",
" },\r\n",
" {\r\n",
" \"$\": \"Cerebrovascular Disorders\"\r\n",
" },\r\n",
" {\r\n",
" \"$\": \"Coronary Disease\"\r\n",
" },\r\n",
" {\r\n",
" \"$\": \"Heart Diseases\"\r\n",
" },\r\n",
" {\r\n",
" \"$\": \"Myocardial Infarction\"\r\n",
" },\r\n",
" {\r\n",
" \"$\": \"Myocardial Ischemia\"\r\n",
" },\r\n",
" {\r\n",
" \"$\": \"Vascular Diseases\"\r\n",
" }\r\n",
" ],\r\n",
" \"arm_group\": [\r\n",
" {\r\n",
" \"arm_group_label\": {\r\n",
" \"$\": 1\r\n",
" },\r\n",
" \"arm_group_type\": {\r\n",
" \"$\": \"Experimental\"\r\n",
" },\r\n",
" \"description\": {\r\n",
" \"$\": \"Vitamin E (600 IU every other day) and aspirin (100 mg every other day)\"\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"arm_group_label\": {\r\n",
" \"$\": 2\r\n",
" },\r\n",
" \"arm_group_type\": {\r\n",
" \"$\": \"Experimental\"\r\n",
" },\r\n",
" \"description\": {\r\n",
" \"$\": \"Vitamin E (600 IU every other day) and placebo\"\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"arm_group_label\": {\r\n",
" \"$\": 3\r\n",
" },\r\n",
" \"arm_group_type\": {\r\n",
" \"$\": \"Experimental\"\r\n",
" },\r\n",
" \"description\": {\r\n",
" \"$\": \"Aspirin (100 mg every other day) and placebo\"\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"arm_group_label\": {\r\n",
" \"$\": 4\r\n",
" },\r\n",
" \"arm_group_type\": {\r\n",
" \"$\": \"Placebo Comparator\"\r\n",
" },\r\n",
" \"description\": {\r\n",
" \"$\": \"Placebo and placebo\"\r\n",
" }\r\n",
" }\r\n",
" ],\r\n",
" \"intervention\": [\r\n",
" {\r\n",
" \"intervention_type\": {\r\n",
" \"$\": \"Drug\"\r\n",
" },\r\n",
" \"intervention_name\": {\r\n",
" \"$\": \"Aspirin\"\r\n",
" },\r\n",
" \"description\": {\r\n",
" \"$\": \"Participants will receive 100 mg of aspirin every other day.\"\r\n",
" },\r\n",
" \"arm_group_label\": [\r\n",
" {\r\n",
" \"$\": 1\r\n",
" },\r\n",
" {\r\n",
" \"$\": 3\r\n",
" }\r\n",
" ]\r\n",
" },\r\n",
" {\r\n",
" \"intervention_type\": {\r\n",
" \"$\": \"Drug\"\r\n",
" },\r\n",
" \"intervention_name\": {\r\n",
" \"$\": \"Vitamin E\"\r\n",
" },\r\n",
" \"description\": {\r\n",
" \"$\": \"Participants will receive 600 IU of vitamin E every other day.\"\r\n",
" },\r\n",
" \"arm_group_label\": [\r\n",
" {\r\n",
" \"$\": 1\r\n",
" },\r\n",
" {\r\n",
" \"$\": 2\r\n",
" }\r\n",
" ]\r\n",
" },\r\n",
" {\r\n",
" \"intervention_type\": {\r\n",
" \"$\": \"Behavioral\"\r\n",
" },\r\n",
" \"intervention_name\": {\r\n",
" \"$\": \"Placebo\"\r\n",
" },\r\n",
" \"description\": {\r\n",
" \"$\": \"Participants will receive placebo.\"\r\n",
" },\r\n",
" \"arm_group_label\": [\r\n",
" {\r\n",
" \"$\": 2\r\n",
" },\r\n",
" {\r\n",
" \"$\": 3\r\n",
" },\r\n",
" {\r\n",
" \"$\": 4\r\n",
" }\r\n",
" ]\r\n",
" }\r\n",
" ],\r\n",
" \"eligibility\": {\r\n",
" \"criteria\": {\r\n",
" \"textblock\": {\r\n",
" \"$\": \"Inclusion Criteria:\\n\\n - Healthy women\\n\\n - No previous history of cardiovascular disease or cancer\\n\\n - No contraindications to aspirin or vitamin E\"\r\n",
" }\r\n",
" },\r\n",
" \"gender\": {\r\n",
" \"$\": \"Female\"\r\n",
" },\r\n",
" \"minimum_age\": {\r\n",
" \"$\": \"45 Years\"\r\n",
" },\r\n",
" \"maximum_age\": {\r\n",
" \"$\": \"N/A\"\r\n",
" },\r\n",
" \"healthy_volunteers\": {\r\n",
" \"$\": \"No\"\r\n",
" }\r\n",
" },\r\n",
" \"overall_official\": {\r\n",
" \"last_name\": {\r\n",
" \"$\": \"Julie Buring\"\r\n",
" },\r\n",
" \"role\": {\r\n",
" \"$\": \"Principal Investigator\"\r\n",
" },\r\n",
" \"affiliation\": {\r\n",
" \"$\": \"Brigham and Women's Hospital\"\r\n",
" }\r\n",
" },\r\n",
" \"reference\": [\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Ridker PM, Miletich JP, Hennekens CH, Buring JE. Ethnic distribution of factor V Leiden in 4047 men and women. Implications for venous thromboembolism screening. JAMA. 1997 Apr 23-30;277(16):1305-7.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 9109469\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Ridker PM, Buring JE, Shih J, Matias M, Hennekens CH. Prospective study of C-reactive protein and the risk of future cardiovascular events among apparently healthy women. Circulation. 1998 Aug 25;98(8):731-3.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 9727541\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Ridker PM, Hennekens CH, Rifai N, Buring JE, Manson JE. Hormone replacement therapy and increased plasma concentration of C-reactive protein. Circulation. 1999 Aug 17;100(7):713-6.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 10449692\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Lee IM, Cook NR, Manson JE, Buring JE, Hennekens CH. Beta-carotene supplementation and incidence of cancer and cardiovascular disease: the Women's Health Study. J Natl Cancer Inst. 1999 Dec 15;91(24):2102-6.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 10601381\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Rexrode KM, Lee IM, Cook NR, Hennekens CH, Buring JE. Baseline characteristics of participants in the Women's Health Study. J Womens Health Gend Based Med. 2000 Jan-Feb;9(1):19-27.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 10718501\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Liu S, Manson JE, Lee IM, Cole SR, Hennekens CH, Willett WC, Buring JE. Fruit and vegetable intake and risk of cardiovascular disease: the Women's Health Study. Am J Clin Nutr. 2000 Oct;72(4):922-8.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 11010932\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Lee IM, Rexrode KM, Cook NR, Manson JE, Buring JE. Physical activity and coronary heart disease in women: is \\\"no pain, no gain\\\" pass\\u00e9? JAMA. 2001 Mar 21;285(11):1447-54.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 11255420\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Pradhan AD, Manson JE, Rifai N, Buring JE, Ridker PM. C-reactive protein, interleukin 6, and risk of developing type 2 diabetes mellitus. JAMA. 2001 Jul 18;286(3):327-34.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 11466099\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Sesso HD, Lee IM, Gaziano JM, Rexrode KM, Glynn RJ, Buring JE. Maternal and paternal history of myocardial infarction and risk of cardiovascular disease in men and women. Circulation. 2001 Jul 24;104(4):393-8.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 11468199\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Ridker PM, Hennekens CH, Buring JE, Rifai N. C-reactive protein and other markers of inflammation in the prediction of cardiovascular disease in women. N Engl J Med. 2000 Mar 23;342(12):836-43.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 10733371\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Blake GJ, Otvos JD, Rifai N, Ridker PM. Low-density lipoprotein particle concentration and size as determined by nuclear magnetic resonance spectroscopy as predictors of cardiovascular disease in women. Circulation. 2002 Oct 8;106(15):1930-7.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 12370215\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Cook NR, Bense\\u00f1or IM, Lotufo PA, Lee IM, Skerrett PJ, Chown MJ, Ajani UA, Manson JE, Buring JE. Migraine and coronary heart disease in women and men. Headache. 2002 Sep;42(8):715-27.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 12390634\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Liu S, Manson JE, Buring JE, Stampfer MJ, Willett WC, Ridker PM. Relation between a diet with a high glycemic load and plasma concentrations of high-sensitivity C-reactive protein in middle-aged women. Am J Clin Nutr. 2002 Mar;75(3):492-8.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 11864854\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Porch JV, Lee IM, Cook NR, Rexrode KM, Burin JE. Estrogen-progestin replacement therapy and breast cancer risk: the Women's Health Study (United States). Cancer Causes Control. 2002 Nov;13(9):847-54.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 12462550\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Ridker PM, Rifai N, Rose L, Buring JE, Cook NR. Comparison of C-reactive protein and low-density lipoprotein cholesterol levels in the prediction of first cardiovascular events. N Engl J Med. 2002 Nov 14;347(20):1557-65.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 12432042\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Ridker PM, Buring JE, Cook NR, Rifai N. C-reactive protein, the metabolic syndrome, and risk of incident cardiovascular events: an 8-year follow-up of 14 719 initially healthy American women. Circulation. 2003 Jan 28;107(3):391-7.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 12551861\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Pradhan AD, Manson JE, Meigs JB, Rifai N, Buring JE, Liu S, Ridker PM. Insulin, proinsulin, proinsulin:insulin ratio, and the risk of developing type 2 diabetes mellitus in women. Am J Med. 2003 Apr 15;114(6):438-44.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 12727576\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Janket SJ, Manson JE, Sesso H, Buring JE, Liu S. A prospective study of sugar intake and risk of type 2 diabetes in women. Diabetes Care. 2003 Apr;26(4):1008-15.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 12663565\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Atiya M, Kurth T, Berger K, Buring JE, Kase CS; Women's Health Study. Interobserver agreement in the classification of stroke in the Women's Health Study. Stroke. 2003 Feb;34(2):565-7.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 12574576\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Ridker PM, Cook N. Clinical usefulness of very high and very low levels of C-reactive protein across the full range of Framingham Risk Scores. Circulation. 2004 Apr 27;109(16):1955-9. Epub 2004 Mar 29.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 15051634\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Albert MA, Glynn RJ, Buring J, Ridker PM. C-reactive protein levels among women of various ethnic groups living in the United States (from the Women's Health Study). Am J Cardiol. 2004 May 15;93(10):1238-42.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 15135696\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Lin J, Zhang SM, Cook NR, Lee IM, Buring JE. Dietary fat and fatty acids and risk of colorectal cancer in women. Am J Epidemiol. 2004 Nov 15;160(10):1011-22.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 15522858\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Weinstein AR, Sesso HD, Lee IM, Cook NR, Manson JE, Buring JE, Gaziano JM. Relationship of physical activity vs body mass index with type 2 diabetes in women. JAMA. 2004 Sep 8;292(10):1188-94.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 15353531\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Christen W, Glynn R, Sperduto R, Chew E, Buring J. Age-related cataract in a randomized trial of beta-carotene in women. Ophthalmic Epidemiol. 2004 Dec;11(5):401-12.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 15590586\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Zhang SM, Buring JE, Lee IM, Cook NR, Ridker PM. C-reactive protein levels are not associated with increased risk for colorectal cancer in women. Ann Intern Med. 2005 Mar 15;142(6):425-32.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 15767620\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Kurth T, Gaziano JM, Rexrode KM, Kase CS, Cook NR, Manson JE, Buring JE. Prospective study of body mass index and risk of stroke in apparently healthy women. Circulation. 2005 Apr 19;111(15):1992-8.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 15837954\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Levitan EB, Ridker PM, Manson JE, Stampfer MJ, Buring JE, Cook NR, Liu S. Association between consumption of beer, wine, and liquor and plasma concentration of high-sensitivity C-reactive protein in women aged 39 to 89 years. Am J Cardiol. 2005 Jul 1;96(1):83-8.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 15979440\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Lee IM, Cook NR, Gaziano JM, Gordon D, Ridker PM, Manson JE, Hennekens CH, Buring JE. Vitamin E in the primary prevention of cardiovascular disease and cancer: the Women's Health Study: a randomized controlled trial. JAMA. 2005 Jul 6;294(1):56-65.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 15998891\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Cook NR, Lee IM, Gaziano JM, Gordon D, Ridker PM, Manson JE, Hennekens CH, Buring JE. Low-dose aspirin in the primary prevention of cancer: the Women's Health Study: a randomized controlled trial. JAMA. 2005 Jul 6;294(1):47-55.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 15998890\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Ridker PM, Rifai N, Cook NR, Bradwin G, Buring JE. Non-HDL cholesterol, apolipoproteins A-I and B100, standard lipid measures, lipid ratios, and CRP as risk factors for cardiovascular disease in women. JAMA. 2005 Jul 20;294(3):326-33.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 16030277\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Ridker PM, Cook NR, Lee IM, Gordon D, Gaziano JM, Manson JE, Hennekens CH, Buring JE. A randomized trial of low-dose aspirin in the primary prevention of cardiovascular disease in women. N Engl J Med. 2005 Mar 31;352(13):1293-304. Epub 2005 Mar 7.\"\r\n",
" },\r\n",
" \"PMID\": {\r\n",
" \"$\": 15753114\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"citation\": {\r\n",
" \"$\": \"Bassuk SS, Ridker PM, Manson JE, Buring JE. Aspirin and cardiovascular disease prevention in women: new findings from the Women's Health Study. Womens Health (Lond). 2005 Jul;1(1):9-10. doi: 10.2217/17455057.1.1.9.\"\r\n",
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" \"$\": \"Myocardial Ischemia\"\r\n",
" },\r\n",
" {\r\n",
" \"$\": \"Cerebrovascular Disorders\"\r\n",
" }\r\n",
" ]\r\n",
" },\r\n",
" \"intervention_browse\": {\r\n",
" \"mesh_term\": [\r\n",
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" \"$\": \"Vitamins\"\r\n",
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" \"$\": \"Vitamin E\"\r\n",
" },\r\n",
" {\r\n",
" \"$\": \"Tocopherols\"\r\n",
" },\r\n",
" {\r\n",
" \"$\": \"Tocotrienols\"\r\n",
" },\r\n",
" {\r\n",
" \"$\": \"alpha-Tocopherol\"\r\n",
" },\r\n",
" {\r\n",
" \"$\": \"Aspirin\"\r\n",
" }\r\n",
" ]\r\n",
" },\r\n",
" \"clinical_results\": {\r\n",
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" \"@group_id\": \"P4\",\r\n",
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" \"$\": \"Both Placebos\"\r\n",
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" \"description\": {\r\n",
" \"$\": \"Placebo aspirin and placebo vitamin E\"\r\n",
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" },\r\n",
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" \"@group_id\": \"P4\",\r\n",
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" \"$\": \"Aspirin(100 mg every other day)and placebo vitamin E\"\r\n",
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" {\r\n",
" \"@group_id\": \"B2\",\r\n",
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" \"$\": \"Placebo aspirin and vitamin E (600 IU every other day\"\r\n",
" }\r\n",
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" \"@group_id\": \"B3\",\r\n",
" \"title\": {\r\n",
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" }\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"B4\",\r\n",
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" \"description\": {\r\n",
" \"$\": \"Placebo aspirin and placebo vitamin E\"\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"B5\",\r\n",
" \"title\": {\r\n",
" \"$\": \"Total\"\r\n",
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" \"description\": {\r\n",
" \"$\": \"Total of all reporting groups\"\r\n",
" }\r\n",
" }\r\n",
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" \"@value\": 9968\r\n",
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" {\r\n",
" \"@group_id\": \"B2\",\r\n",
" \"@value\": 9971\r\n",
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" {\r\n",
" \"@group_id\": \"B3\",\r\n",
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" {\r\n",
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" \"title\": {\r\n",
" \"$\": \"<=18 years\"\r\n",
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" }\r\n",
" },\r\n",
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" \"@group_id\": \"B1\",\r\n",
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" },\r\n",
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" \"@group_id\": \"B1\",\r\n",
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" },\r\n",
" \"param\": {\r\n",
" \"$\": \"Mean\"\r\n",
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" }\r\n",
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" }\r\n",
" },\r\n",
" {\r\n",
" \"title\": {\r\n",
" \"$\": \"Sex: Female, Male\"\r\n",
" },\r\n",
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" },\r\n",
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" \"category\": [\r\n",
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" \"title\": {\r\n",
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" {\r\n",
" \"@group_id\": \"B1\",\r\n",
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" \"@value\": 39876\r\n",
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" ]\r\n",
" }\r\n",
" },\r\n",
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" \"title\": {\r\n",
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" {\r\n",
" \"@group_id\": \"B5\",\r\n",
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" }\r\n",
" }\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"title\": {\r\n",
" \"$\": \"Region of Enrollment\"\r\n",
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" \"type\": {\r\n",
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" \"title\": {\r\n",
" \"$\": \"Number of Participants With Major Cardiovascular Events (a Combined Endpoint of Nonfatal Myocardial Infarction, Nonfatal Stroke, and Total Cardiovascular Death)\"\r\n",
" },\r\n",
" \"time_frame\": {\r\n",
" \"$\": \"Average follow-up 10.1 years\"\r\n",
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" \"@group_id\": \"O1\",\r\n",
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" }\r\n",
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" {\r\n",
" \"@group_id\": \"O2\",\r\n",
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" \"$\": \"Vitamin E Only\"\r\n",
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" \"$\": \"Placebo aspirin and vitamin E (600 IU every other day\"\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"O3\",\r\n",
" \"title\": {\r\n",
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" }\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"O4\",\r\n",
" \"title\": {\r\n",
" \"$\": \"Both Placebos\"\r\n",
" },\r\n",
" \"description\": {\r\n",
" \"$\": \"Placebo aspirin and placebo vitamin E\"\r\n",
" }\r\n",
" }\r\n",
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" },\r\n",
" \"measure\": {\r\n",
" \"title\": {\r\n",
" \"$\": \"Number of Participants With Major Cardiovascular Events (a Combined Endpoint of Nonfatal Myocardial Infarction, Nonfatal Stroke, and Total Cardiovascular Death)\"\r\n",
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" \"@lower_limit\": 0.82,\r\n",
" \"@upper_limit\": 1.05\r\n",
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" },\r\n",
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" \"title\": {\r\n",
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" \"@value\": 113,\r\n",
" \"@lower_limit\": 0.69,\r\n",
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" {\r\n",
" \"@group_id\": \"O2\",\r\n",
" \"@value\": 133,\r\n",
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" {\r\n",
" \"title\": {\r\n",
" \"$\": \"Myocardial infarction\"\r\n",
" },\r\n",
" \"category_list\": {\r\n",
" \"category\": {\r\n",
" \"measurement_list\": {\r\n",
" \"measurement\": [\r\n",
" {\r\n",
" \"@group_id\": \"O1\",\r\n",
" \"@value\": 96,\r\n",
" \"@lower_limit\": 0.84,\r\n",
" \"@upper_limit\": 1.25\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"O2\",\r\n",
" \"@value\": 94,\r\n",
" \"@lower_limit\": 0.82,\r\n",
" \"@upper_limit\": 1.23\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"O3\",\r\n",
" \"@value\": 102\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"O4\",\r\n",
" \"@value\": 99\r\n",
" }\r\n",
" ]\r\n",
" }\r\n",
" }\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"title\": {\r\n",
" \"$\": \"Cardiovascular death\"\r\n",
" },\r\n",
" \"category_list\": {\r\n",
" \"category\": {\r\n",
" \"measurement_list\": {\r\n",
" \"measurement\": [\r\n",
" {\r\n",
" \"@group_id\": \"O1\",\r\n",
" \"@value\": 66,\r\n",
" \"@lower_limit\": 0.74,\r\n",
" \"@upper_limit\": 1.22\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"O2\",\r\n",
" \"@value\": 52,\r\n",
" \"@lower_limit\": 0.59,\r\n",
" \"@upper_limit\": 0.98\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"O3\",\r\n",
" \"@value\": 54\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"O4\",\r\n",
" \"@value\": 74\r\n",
" }\r\n",
" ]\r\n",
" }\r\n",
" }\r\n",
" }\r\n",
" }\r\n",
" ]\r\n",
" }\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"type\": {\r\n",
" \"$\": \"Primary\"\r\n",
" },\r\n",
" \"title\": {\r\n",
" \"$\": \"Number of Participants With Cancer, Excluding Nonmelanoma Skin Cancer\"\r\n",
" },\r\n",
" \"time_frame\": {\r\n",
" \"$\": \"Average follow-up 10.1 years\"\r\n",
" },\r\n",
" \"group_list\": {\r\n",
" \"group\": [\r\n",
" {\r\n",
" \"@group_id\": \"O1\",\r\n",
" \"title\": {\r\n",
" \"$\": \"Aspirin Only\"\r\n",
" },\r\n",
" \"description\": {\r\n",
" \"$\": \"Aspirin(100 mg every other day)and placebo vitamin E\"\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"O2\",\r\n",
" \"title\": {\r\n",
" \"$\": \"Vitamin E Only\"\r\n",
" },\r\n",
" \"description\": {\r\n",
" \"$\": \"Placebo aspirin and vitamin E (600 IU every other day\"\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"O3\",\r\n",
" \"title\": {\r\n",
" \"$\": \"Aspirin + Vitamin E\"\r\n",
" },\r\n",
" \"description\": {\r\n",
" \"$\": \"Aspirin (100 mg every other day) and vitamin E (600 IU every other day)\"\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"O4\",\r\n",
" \"title\": {\r\n",
" \"$\": \"Both Placebos\"\r\n",
" },\r\n",
" \"description\": {\r\n",
" \"$\": \"Placebo aspirin and placebo vitamin E\"\r\n",
" }\r\n",
" }\r\n",
" ]\r\n",
" },\r\n",
" \"measure\": {\r\n",
" \"title\": {\r\n",
" \"$\": \"Number of Participants With Cancer, Excluding Nonmelanoma Skin Cancer\"\r\n",
" },\r\n",
" \"units\": {\r\n",
" \"$\": \"participants\"\r\n",
" },\r\n",
" \"param\": {\r\n",
" \"$\": \"Number\"\r\n",
" },\r\n",
" \"analyzed_list\": {\r\n",
" \"analyzed\": {\r\n",
" \"units\": {\r\n",
" \"$\": \"Participants\"\r\n",
" },\r\n",
" \"scope\": {\r\n",
" \"$\": \"Measure\"\r\n",
" },\r\n",
" \"count_list\": {\r\n",
" \"count\": [\r\n",
" {\r\n",
" \"@group_id\": \"O1\",\r\n",
" \"@value\": 9968\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"O2\",\r\n",
" \"@value\": 9971\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"O3\",\r\n",
" \"@value\": 9966\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"O4\",\r\n",
" \"@value\": 9971\r\n",
" }\r\n",
" ]\r\n",
" }\r\n",
" }\r\n",
" },\r\n",
" \"class_list\": {\r\n",
" \"class\": [\r\n",
" {\r\n",
" \"title\": {\r\n",
" \"$\": \"Total invasive cancer\"\r\n",
" },\r\n",
" \"category_list\": {\r\n",
" \"category\": {\r\n",
" \"measurement_list\": {\r\n",
" \"measurement\": [\r\n",
" {\r\n",
" \"@group_id\": \"O1\",\r\n",
" \"@value\": 722,\r\n",
" \"@lower_limit\": 0.94,\r\n",
" \"@upper_limit\": 1.08\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"O2\",\r\n",
" \"@value\": 721,\r\n",
" \"@lower_limit\": 0.94,\r\n",
" \"@upper_limit\": 1.08\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"O3\",\r\n",
" \"@value\": 716\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"O4\",\r\n",
" \"@value\": 706\r\n",
" }\r\n",
" ]\r\n",
" }\r\n",
" }\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"title\": {\r\n",
" \"$\": \"Cancer death\"\r\n",
" },\r\n",
" \"category_list\": {\r\n",
" \"category\": {\r\n",
" \"measurement_list\": {\r\n",
" \"measurement\": [\r\n",
" {\r\n",
" \"@group_id\": \"O1\",\r\n",
" \"@value\": 132,\r\n",
" \"@lower_limit\": 0.81,\r\n",
" \"@upper_limit\": 1.11\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"O2\",\r\n",
" \"@value\": 156,\r\n",
" \"@lower_limit\": 0.95,\r\n",
" \"@upper_limit\": 1.32\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"O3\",\r\n",
" \"@value\": 152\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"O4\",\r\n",
" \"@value\": 143\r\n",
" }\r\n",
" ]\r\n",
" }\r\n",
" }\r\n",
" }\r\n",
" }\r\n",
" ]\r\n",
" }\r\n",
" }\r\n",
" }\r\n",
" ]\r\n",
" },\r\n",
" \"reported_events\": {\r\n",
" \"group_list\": {\r\n",
" \"group\": [\r\n",
" {\r\n",
" \"@group_id\": \"E1\",\r\n",
" \"title\": {\r\n",
" \"$\": \"Aspirin Only\"\r\n",
" },\r\n",
" \"description\": {\r\n",
" \"$\": \"Aspirin(100 mg every other day)and placebo vitamin E\"\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"E2\",\r\n",
" \"title\": {\r\n",
" \"$\": \"Vitamin E Only\"\r\n",
" },\r\n",
" \"description\": {\r\n",
" \"$\": \"Placebo aspirin and vitamin E (600 IU every other day\"\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"E3\",\r\n",
" \"title\": {\r\n",
" \"$\": \"Aspirin + Vitamin E\"\r\n",
" },\r\n",
" \"description\": {\r\n",
" \"$\": \"Aspirin (100 mg every other day) and vitamin E (600 IU every other day)\"\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"E4\",\r\n",
" \"title\": {\r\n",
" \"$\": \"Both Placebos\"\r\n",
" },\r\n",
" \"description\": {\r\n",
" \"$\": \"Placebo aspirin and placebo vitamin E\"\r\n",
" }\r\n",
" }\r\n",
" ]\r\n",
" },\r\n",
" \"serious_events\": {\r\n",
" \"default_vocab\": {\r\n",
" \"$\": \"ICD\"\r\n",
" },\r\n",
" \"default_assessment\": {\r\n",
" \"$\": \"Systematic Assessment\"\r\n",
" },\r\n",
" \"category_list\": {\r\n",
" \"category\": [\r\n",
" {\r\n",
" \"title\": {\r\n",
" \"$\": \"Total\"\r\n",
" },\r\n",
" \"event_list\": {\r\n",
" \"event\": {\r\n",
" \"sub_title\": {\r\n",
" \"$\": \"Total, serious adverse events\"\r\n",
" },\r\n",
" \"counts\": [\r\n",
" {\r\n",
" \"@group_id\": \"E1\",\r\n",
" \"@subjects_affected\": 27,\r\n",
" \"@subjects_at_risk\": 9968\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"E2\",\r\n",
" \"@subjects_affected\": 20,\r\n",
" \"@subjects_at_risk\": 9971\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"E3\",\r\n",
" \"@subjects_affected\": 24,\r\n",
" \"@subjects_at_risk\": 9966\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"E4\",\r\n",
" \"@subjects_affected\": 21,\r\n",
" \"@subjects_at_risk\": 9971\r\n",
" }\r\n",
" ]\r\n",
" }\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"title\": {\r\n",
" \"$\": \"Blood and lymphatic system disorders\"\r\n",
" },\r\n",
" \"event_list\": {\r\n",
" \"event\": {\r\n",
" \"sub_title\": {\r\n",
" \"$\": \"hemorrhagic stroke\"\r\n",
" },\r\n",
" \"counts\": [\r\n",
" {\r\n",
" \"@group_id\": \"E1\",\r\n",
" \"@events\": 27,\r\n",
" \"@subjects_affected\": 27,\r\n",
" \"@subjects_at_risk\": 9968\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"E2\",\r\n",
" \"@events\": 20,\r\n",
" \"@subjects_affected\": 20,\r\n",
" \"@subjects_at_risk\": 9971\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"E3\",\r\n",
" \"@events\": 24,\r\n",
" \"@subjects_affected\": 24,\r\n",
" \"@subjects_at_risk\": 9966\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"E4\",\r\n",
" \"@events\": 21,\r\n",
" \"@subjects_affected\": 21,\r\n",
" \"@subjects_at_risk\": 9971\r\n",
" }\r\n",
" ]\r\n",
" }\r\n",
" }\r\n",
" }\r\n",
" ]\r\n",
" }\r\n",
" },\r\n",
" \"other_events\": {\r\n",
" \"frequency_threshold\": {\r\n",
" \"$\": 5\r\n",
" },\r\n",
" \"default_vocab\": {\r\n",
" \"$\": \"ICD\"\r\n",
" },\r\n",
" \"default_assessment\": {\r\n",
" \"$\": \"Systematic Assessment\"\r\n",
" },\r\n",
" \"category_list\": {\r\n",
" \"category\": [\r\n",
" {\r\n",
" \"title\": {\r\n",
" \"$\": \"Total\"\r\n",
" },\r\n",
" \"event_list\": {\r\n",
" \"event\": {\r\n",
" \"sub_title\": {\r\n",
" \"$\": \"Total, other adverse events\"\r\n",
" },\r\n",
" \"counts\": [\r\n",
" {\r\n",
" \"@group_id\": \"E1\",\r\n",
" \"@subjects_affected\": 5969,\r\n",
" \"@subjects_at_risk\": 9968\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"E2\",\r\n",
" \"@subjects_affected\": 5915,\r\n",
" \"@subjects_at_risk\": 9971\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"E3\",\r\n",
" \"@subjects_affected\": 5887,\r\n",
" \"@subjects_at_risk\": 9966\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"E4\",\r\n",
" \"@subjects_affected\": 6000,\r\n",
" \"@subjects_at_risk\": 9971\r\n",
" }\r\n",
" ]\r\n",
" }\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"title\": {\r\n",
" \"$\": \"Blood and lymphatic system disorders\"\r\n",
" },\r\n",
" \"event_list\": {\r\n",
" \"event\": [\r\n",
" {\r\n",
" \"sub_title\": {\r\n",
" \"$\": \"hematuria\"\r\n",
" },\r\n",
" \"counts\": [\r\n",
" {\r\n",
" \"@group_id\": \"E1\",\r\n",
" \"@events\": 1534,\r\n",
" \"@subjects_affected\": 1534,\r\n",
" \"@subjects_at_risk\": 9968\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"E2\",\r\n",
" \"@events\": 1467,\r\n",
" \"@subjects_affected\": 1467,\r\n",
" \"@subjects_at_risk\": 9971\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"E3\",\r\n",
" \"@events\": 1505,\r\n",
" \"@subjects_affected\": 1505,\r\n",
" \"@subjects_at_risk\": 9966\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"E4\",\r\n",
" \"@events\": 1411,\r\n",
" \"@subjects_affected\": 1411,\r\n",
" \"@subjects_at_risk\": 9971\r\n",
" }\r\n",
" ]\r\n",
" },\r\n",
" {\r\n",
" \"sub_title\": {\r\n",
" \"$\": \"easy bruising\"\r\n",
" },\r\n",
" \"counts\": [\r\n",
" {\r\n",
" \"@group_id\": \"E1\",\r\n",
" \"@events\": 5297,\r\n",
" \"@subjects_affected\": 5297,\r\n",
" \"@subjects_at_risk\": 9968\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"E2\",\r\n",
" \"@events\": 4247,\r\n",
" \"@subjects_affected\": 4247,\r\n",
" \"@subjects_at_risk\": 9971\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"E3\",\r\n",
" \"@events\": 5263,\r\n",
" \"@subjects_affected\": 5263,\r\n",
" \"@subjects_at_risk\": 9966\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"E4\",\r\n",
" \"@events\": 4247,\r\n",
" \"@subjects_affected\": 4247,\r\n",
" \"@subjects_at_risk\": 9971\r\n",
" }\r\n",
" ]\r\n",
" },\r\n",
" {\r\n",
" \"sub_title\": {\r\n",
" \"$\": \"epistaxis\"\r\n",
" },\r\n",
" \"counts\": [\r\n",
" {\r\n",
" \"@group_id\": \"E1\",\r\n",
" \"@events\": 1854,\r\n",
" \"@subjects_affected\": 1854,\r\n",
" \"@subjects_at_risk\": 9968\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"E2\",\r\n",
" \"@events\": 1703,\r\n",
" \"@subjects_affected\": 1703,\r\n",
" \"@subjects_at_risk\": 9971\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"E3\",\r\n",
" \"@events\": 1947,\r\n",
" \"@subjects_affected\": 1947,\r\n",
" \"@subjects_at_risk\": 9966\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"E4\",\r\n",
" \"@events\": 1618,\r\n",
" \"@subjects_affected\": 1618,\r\n",
" \"@subjects_at_risk\": 9971\r\n",
" }\r\n",
" ]\r\n",
" }\r\n",
" ]\r\n",
" }\r\n",
" },\r\n",
" {\r\n",
" \"title\": {\r\n",
" \"$\": \"Gastrointestinal disorders\"\r\n",
" },\r\n",
" \"event_list\": {\r\n",
" \"event\": {\r\n",
" \"sub_title\": {\r\n",
" \"$\": \"report of GI upset\"\r\n",
" },\r\n",
" \"counts\": [\r\n",
" {\r\n",
" \"@group_id\": \"E1\",\r\n",
" \"@events\": 5969,\r\n",
" \"@subjects_affected\": 5969,\r\n",
" \"@subjects_at_risk\": 9968\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"E2\",\r\n",
" \"@events\": 5915,\r\n",
" \"@subjects_affected\": 5915,\r\n",
" \"@subjects_at_risk\": 9971\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"E3\",\r\n",
" \"@events\": 5887,\r\n",
" \"@subjects_affected\": 5887,\r\n",
" \"@subjects_at_risk\": 9966\r\n",
" },\r\n",
" {\r\n",
" \"@group_id\": \"E4\",\r\n",
" \"@events\": 6000,\r\n",
" \"@subjects_affected\": 6000,\r\n",
" \"@subjects_at_risk\": 9971\r\n",
" }\r\n",
" ]\r\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
" }\r\n",
" }\r\n",
" }\r\n",
" ]\r\n",
" }\r\n",
" }\r\n",
" },\r\n",
" \"certain_agreements\": {\r\n",
" \"pi_employee\": {\r\n",
" \"$\": \"All Principal Investigators ARE employed by the organization sponsoring the study.\"\r\n",
" },\r\n",
" \"restrictive_agreement\": {\r\n",
" \"$\": \"There is NOT an agreement between Principal Investigators and the Sponsor (or its agents) that restricts the PI's rights to discuss or publish trial results after the trial is completed.\"\r\n",
" }\r\n",
" },\r\n",
" \"point_of_contact\": {\r\n",
" \"name_or_title\": {\r\n",
" \"$\": \"Julie E. Buring\"\r\n",
" },\r\n",
" \"organization\": {\r\n",
" \"$\": \"Brigham and Women's Hospital\"\r\n",
" },\r\n",
" \"phone\": {\r\n",
" \"$\": \"617 732 4965\"\r\n",
" },\r\n",
" \"email\": {\r\n",
" \"$\": \"jburing@rics.bwh.harvard.edu\"\r\n",
" }\r\n",
" }\r\n",
" }\r\n",
" }\r\n",
"}"
]
}
],
"source": [
"!python -m xmljson -d badgerfish ./data/search_result/NCT00000479.xml"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {},
"outputs": [],
"source": [
"!for f in $(ls | grep '.xml'); do python -m xmljson -d yahoo $f > $json/f.json ; done"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": 21,
"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>brief_summary</th>\n",
" <th>detailed_description</th>\n",
" <th>intervention</th>\n",
" <th>condition</th>\n",
" <th>enrollment</th>\n",
" <th>eligibility</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
"Empty DataFrame\n",
"Columns: [brief_summary, detailed_description, intervention, condition, enrollment, eligibility]\n",
"Index: []"
]
},
"execution_count": 21,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"df.head()"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"required_header {}\n",
"id_info {}\n",
"brief_title {}\n",
"sponsors {}\n",
"source {}\n",
"brief_summary {}\n",
"detailed_description {}\n",
"overall_status {}\n",
"start_date {}\n",
"completion_date {'type': 'Actual'}\n",
"primary_completion_date {'type': 'Actual'}\n",
"phase {}\n",
"study_type {}\n",
"has_expanded_access {}\n",
"study_design_info {}\n",
"condition {}\n",
"condition {}\n",
"condition {}\n",
"condition {}\n",
"intervention {}\n",
"intervention {}\n",
"eligibility {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
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"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"reference {}\n",
"verification_date {}\n",
"study_first_submitted {}\n",
"study_first_submitted_qc {}\n",
"study_first_posted {'type': 'Estimate'}\n",
"last_update_submitted {}\n",
"last_update_submitted_qc {}\n",
"last_update_posted {'type': 'Estimate'}\n",
"responsible_party {}\n",
"condition_browse {}\n",
"intervention_browse {}\n"
]
}
],
"source": [
"for child in root:\n",
" print(child.tag, child.attrib)"
]
},
{
"cell_type": "code",
"execution_count": 23,
"metadata": {},
"outputs": [
{
"ename": "IndentationError",
"evalue": "expected an indented block (<ipython-input-23-55b1bc950e52>, line 5)",
"output_type": "error",
"traceback": [
"\u001b[0;36m File \u001b[0;32m\"<ipython-input-23-55b1bc950e52>\"\u001b[0;36m, line \u001b[0;32m5\u001b[0m\n\u001b[0;31m df = df.append(\u001b[0m\n\u001b[0m ^\u001b[0m\n\u001b[0;31mIndentationError\u001b[0m\u001b[0;31m:\u001b[0m expected an indented block\n"
]
}
],
"source": [
"dfcols = ['clinical_study', 'nct_id', 'brief_title']\n",
"df = pd.DataFrame(columns=dfcols)\n",
"\n",
"for i in etree.iter(tag='data'):\n",
"df = df.append(\n",
" pd.Series([i.get('id'), i.get('name')], index=dfcols),\n",
" ignore_index=True)\n",
"df.head()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"trials.head()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Retrieve Tweets\n",
"MaxTweets = 10000000\n",
"tweetsPerQry = 100\n",
"fName = 'tweets.txt' # Storage name\n",
"\n",
"tweetCount = 0\n",
"print(\"Downloading max {0} tweets\".format(MaxTweets))\n",
"with open(fName, 'w') as f:\n",
" for tweet in tweepy.Cursor(api.search,q=query, wait_on_rate_limit=True).items(MaxTweets) : \n",
"\n",
" # Verify the tweet has place info before writing\n",
" if tweet.place is not None:\n",
" \n",
" #Write to the text file, and add one to the number of tweets\n",
" f.write(jsonpickle.encode(tweet._json, unpicklable=False) + '\\n')\n",
" tweetCount += 1\n",
"\n",
" #Display how many tweets we have collected\n",
" print(\"Downloaded {0} tweets\".format(tweetCount))\n",
" "
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Checking the data\n",
"tweet._json"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"max_id = -1\n",
"tweetCount = 0\n",
"with open('PoGo_USA_Tutorial.json', 'w') as f:\n",
" #While we still want to collect more tweets\n",
" while tweetCount < MaxTweets:\n",
" try:\n",
" #Look for more tweets, resuming where we left off\n",
" if max_id <= 0:\n",
" new_tweets = api.search(q=query, count=tweetsPerQry)\n",
" else:\n",
" new_tweets = api.search(q=query, count=tweetsPerQry, max_id=str(max_id - 1))\n",
" \n",
" #If we didn't find any exit the loop\n",
" if not new_tweets:\n",
" print(\"No more tweets found\")\n",
" break\n",
" \n",
" #Write the JSON output of any new tweets we found to the output file\n",
" for tweet in new_tweets:\n",
" \n",
" #Make sure the tweet has place info before writing\n",
" if (tweet.place is not None) and (tweetCount < MaxTweets):\n",
" f.write(jsonpickle.encode(tweet._json, unpicklable=False) +\n",
" '\\n')\n",
" tweetCount += 1\n",
" \n",
" #Display how many tweets we have collected\n",
" print(\"Downloaded {0} tweets\".format(tweetCount))\n",
" \n",
" #Record the id of the last tweet we looked at\n",
" max_id = new_tweets[-1].id\n",
" \n",
" except tweepy.TweepError as e:\n",
" \n",
" #Print the error and continue searching\n",
" print(\"some error : \" + str(e))\n",
"\n",
"\n",
"print (\"Downloaded {0} tweets, Saved to {1}\".format(tweetCount, fName))"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"#search for multiple phrases using OR (for Pharma companies)\n",
"Allquery = \"'Johnson & Johnson' or 'J & J' or 'J&J' or 'JNJ' or '$JNJ' \\\n",
" or 'Pfizer' or 'pfizer' or 'PFE' or '$PFE' \\\n",
" or 'Novartis' or 'novartis' or 'NOVN' or '$NOVN' \\\n",
" or 'Roche' or 'roche' or 'ROG' or '$ROG' \\\n",
" or 'Merck & Co.' or 'Merck' or 'MRK' or '$MRK' \\\n",
" or 'AbbVie' or 'abbvie' or 'ABBV' or '$ABBV' \\\n",
" or 'Eli Lilly' or 'EliLilly' or 'LLY' or '$LLY' \\\n",
" or 'Sanofi' or 'sanofi' or 'SAN' or '$SAN' \\\n",
" or 'AstraZeneca' or 'astrazeneca' or 'AZN' or '$AZN' \\\n",
" or 'GlaxoSmithKline' or 'GSK' or '$GSK'\""
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
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"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
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}