Document is here. https://www.ncbi.nlm.nih.gov/books/NBK25501/
https://www.nlm.nih.gov/databases/download/terms_and_conditions.html
outputimage
import math
import matplotlib.pyplot as plt
import matplotlib.cm as cm
import numpy as np
import pandas as pd
import plotly
import plotly.express as px
import requests
import urllib.parse
import uuid
import xml.etree.ElementTree as ET
from collections import OrderedDict
from sklearn.cluster import MiniBatchKMeans
from sklearn.feature_extraction.text import TfidfVectorizer
from sklearn.decomposition import PCA
from sklearn.manifold import TSNE
from tqdm import tqdm_notebook as tqdm
plotly.offline.init_notebook_mode(connected=False)
# const
BASEURL_INFO = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi'
BASEURL_SRCH = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi'
BASEURL_FTCH = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi'
# parameters
SOURCE_DB = 'pubmed'
TERM = 'cancer'
DATE_TYPE = 'pdat' # Type of date used to limit a search. The allowed values vary between Entrez databases, but common values are 'mdat' (modification date), 'pdat' (publication date) and 'edat' (Entrez date). Generally an Entrez database will have only two allowed values for datetype.
MIN_DATE = '2018/01/01' # yyyy/mm/dd
MAX_DATE = '2019/12/31' # yyyy/mm/dd
SEP = '|'
BATCH_NUM = 1000
# seed
RANDOM_STATE = 42
np.random.seed(RANDOM_STATE)
'''
make query function
base_url: base_url
params: parameter dictionary
ex) {key1: value1, key2: value2}
'''
def mkquery(base_url, params):
base_url += '?'
for key, value in zip(params.keys(), params.values()):
base_url += '{key}={value}&'.format(key=key, value=value)
url = base_url[0:len(base_url) - 1]
print('request url is: ' + url)
return url
'''
getXmlFromURL
(mkquery wrapper)
base_url: base_url
params: parameter dictionary
ex) {key1: value1, key2: value2}
'''
def getXmlFromURL(base_url, params):
response = requests.get(mkquery(base_url, params))
return ET.fromstring(response.text)
'''
getTextFromNode
root: Xml root node
path: XPath
fill: fill na string
mode: 0 = text, 1 = attribute
attrib: attribute name
'''
def getTextFromNode(root, path, fill='', mode=0, attrib='attribute'):
if (root.find(path) == None):
return fill
else:
if mode == 0:
return root.find(path).text
if mode == 1:
return root.find(path).get(attrib)
# example
rootXml = getXmlFromURL(BASEURL_INFO, {'db': SOURCE_DB})
request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=pubmed
# Info API
rootXml = getXmlFromURL(BASEURL_INFO, {'db': SOURCE_DB})
print(rootXml.find('DbInfo').find('Count').text)
print(rootXml.find('DbInfo').find('LastUpdate').text)
request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=pubmed 30214909 2019/10/13 20:30
# get xml
rootXml = getXmlFromURL(BASEURL_SRCH, {
'db': SOURCE_DB,
'term': TERM,
'usehistory': 'y',
'datetype': DATE_TYPE,
'mindate': MIN_DATE,
'maxdate': MAX_DATE})
request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=cancer&usehistory=y&datetype=pdat&mindate=2018/01/01&maxdate=2019/12/31
# get querykey and webenv
Count = rootXml.find('Count').text
QueryKey = rootXml.find('QueryKey').text
WebEnv = urllib.parse.quote(rootXml.find('WebEnv').text)
print('total Count: ', Count)
print('QueryKey : ', QueryKey)
print('WebEnv : ', WebEnv)
total Count: 338233 QueryKey : 1 WebEnv : NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore
articleDics = []
authorArticleDics = []
authorAffiliationDics = []
def pushData(rootXml):
for article in rootXml.iter('PubmedArticle'):
# get article info
articleDic = {
'PMID' : getTextFromNode(article, 'MedlineCitation/PMID', ''),
'JournalTitle' : getTextFromNode(article, 'MedlineCitation/Article/Journal/Title', ''),
'Title' : getTextFromNode(article, 'MedlineCitation/Article/ArticleTitle', ''),
'doi' : getTextFromNode(article, 'MedlineCitation/Article/ELocationID[@EIdType="doi"]', ''),
'Abstract' : getTextFromNode(article, 'MedlineCitation/Article/Abstract/AbstractText', ''),
# if you want to get data in flat(denormalized), uncomment below. but it's difficult to use for analytics.
# 'Authors' : SEP.join([author.find('ForeName').text + ' ' + author.find('LastName').text if author.find('CollectiveName') == None else author.find('CollectiveName').text for author in article.findall('MedlineCitation/Article/AuthorList/')]),
# 'AuthorIdentifiers' : SEP.join([getTextFromNode(author, 'Identifier', 'None') for author in article.findall('MedlineCitation/Article/AuthorList/')]),
# 'AuthorIdentifierSources' : SEP.join([getTextFromNode(author, 'Identifier', 'None', 1, 'Source') for author in article.findall('MedlineCitation/Article/AuthorList/')]),
'Language' : getTextFromNode(article, 'MedlineCitation/Article/Language', ''),
'Year_A' : getTextFromNode(article, 'MedlineCitation/Article/ArticleDate/Year', ''),
'Month_A' : getTextFromNode(article, 'MedlineCitation/Article/ArticleDate/Month', ''),
'Day_A' : getTextFromNode(article, 'MedlineCitation/Article/ArticleDate/Day', ''),
'Year_PM' : getTextFromNode(article, 'PubmedData/History/PubMedPubDate[@PubStatus="pubmed"]/Year', ''),
'Month_PM' : getTextFromNode(article, 'PubmedData/History/PubMedPubDate[@PubStatus="pubmed"]/Month', ''),
'Day_PM' : getTextFromNode(article, 'PubmedData/History/PubMedPubDate[@PubStatus="pubmed"]/Day', ''),
'Status' : getTextFromNode(article, './PubmedData/PublicationStatus', ''),
'MeSH' : SEP.join([getTextFromNode(mesh, 'DescriptorName') for mesh in article.findall('MedlineCitation/MeshHeadingList/')]),
'MeSH_UI' : SEP.join([getTextFromNode(mesh, 'DescriptorName', '', 1, 'UI') for mesh in article.findall('MedlineCitation/MeshHeadingList/')]),
'Keyword' : SEP.join([keyword.text if keyword.text != None else '' for keyword in article.findall('MedlineCitation/KeywordList/')])
}
articleDics.append(OrderedDict(articleDic))
if article.find('MedlineCitation/MeshHeadingList/MeshHeading/') != None:
tmp = article
# get author info
for author in article.findall('MedlineCitation/Article/AuthorList/'):
# publish author ID
# * It's only random id. not use for identify author. if you want to identify author, you can use identifier.
authorId = str(uuid.uuid4())
# author article
authorArticleDic = {
'authorId' : authorId,
'PMID' : getTextFromNode(article, 'MedlineCitation/PMID', ''),
'name' : getTextFromNode(author, 'ForeName') + ' ' + getTextFromNode(author,'LastName') if author.find('CollectiveName') == None else author.find('CollectiveName').text,
'identifier' : getTextFromNode(author, 'Identifier', '') ,
'identifierSource' : getTextFromNode(author, 'Identifier', '', 1, 'Source')
}
authorArticleDics.append(OrderedDict(authorArticleDic))
# author affiliation(author: affiliation = 1 : n)
if author.find('./AffiliationInfo') != None:
for affiliation in author.findall('./AffiliationInfo'):
authorAffiliationDic = {
'authorId' : authorId,
'affiliation' : getTextFromNode(affiliation, 'Affiliation', '') ,
}
authorAffiliationDics.append(OrderedDict(authorAffiliationDic))
# ceil
iterCount = math.ceil(int(Count) / BATCH_NUM)
# get all data
for i in tqdm(range(iterCount)):
rootXml = getXmlFromURL(BASEURL_FTCH, {
'db': SOURCE_DB,
'query_key': QueryKey,
'WebEnv': WebEnv,
'retstart': i * BATCH_NUM,
'retmax': BATCH_NUM,
'retmode': 'xml'})
pushData(rootXml)
HBox(children=(IntProgress(value=0, max=339), HTML(value='')))
request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=0&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=1000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=2000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=3000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=4000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=5000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=6000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=7000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=8000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=9000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=10000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=11000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=12000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=13000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=14000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=15000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=16000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=17000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=18000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=19000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=20000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=21000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=22000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=23000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=24000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=25000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=26000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=27000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=28000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=29000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=30000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=31000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=32000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=33000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=34000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=35000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=36000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=37000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=38000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=39000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=40000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=41000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=42000&retmax=1000&retmode=xml request url is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_139733426_130.14.18.48_9001_1571037702_959831376_0MetA0_S_MegaStore&retstart=43000&retmax=1000&retmode=xml request url is: 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# article
df_article = pd.DataFrame(articleDics)
df_article.head(10)
PMID | JournalTitle | Title | doi | Abstract | Language | Year_A | Month_A | Day_A | Year_PM | Month_PM | Day_PM | Status | MeSH | MeSH_UI | Keyword | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | 31606007 | Mutagenesis | Genetic variants in taste-related genes and ri... | 10.1093/mutage/gez032 | Pancreatic ductal adenocarcinoma is an aggress... | eng | 2019 | 10 | 12 | 2019 | 10 | 13 | aheadofprint | |||
1 | 31606005 | European journal of oncology nursing : the off... | Enhancing the cancer caregiving experience: Bu... | 10.1016/j.ejon.2019.09.004 | The purpose of this study was to explore the d... | eng | 2019 | 09 | 10 | 2019 | 10 | 13 | aheadofprint | Benefit|Dyad|Family caregiver|Mixed methods|Mu... | ||
2 | 31605953 | Biomedicine & pharmacotherapy = Biomedecine & ... | Dual roles of glutathione S-transferase mu 1 i... | 10.1016/j.biopha.2019.109532 | Reactive oxygen species (ROS) are implicated i... | eng | 2019 | 10 | 09 | 2019 | 10 | 13 | aheadofprint | GSTM1|Glutathione|Hepatocellular carcinoma|Rea... | ||
3 | 31605952 | Biomedicine & pharmacotherapy = Biomedecine & ... | Reversal of drug resistance by JS-K and nitric... | 10.1016/j.biopha.2019.109468 | Development of resistance to chemotherapy drug... | eng | 2019 | 10 | 09 | 2019 | 10 | 13 | aheadofprint | Adriamycin|Breast cancer resistance protein|JS... | ||
4 | 31605946 | iScience | Genetic Landscape of Somatic Mutations in a La... | 10.1016/j.isci.2019.09.030 | Sporadic Medullary Thyroid Carcinoma (sMTC) is... | eng | 2019 | 09 | 26 | 2019 | 10 | 13 | aheadofprint | Biological Sciences|Cancer|Genomics | ||
5 | 31605942 | iScience | Inferring Disease-Associated MicroRNAs Using S... | 10.1016/j.isci.2019.09.013 | MicroRNAs (miRNAs) play crucial roles in biolo... | eng | 2019 | 09 | 16 | 2019 | 10 | 13 | aheadofprint | Biocomputational Method|Computer Modeling|Dise... | ||
6 | 31605927 | Bioorganic chemistry | Adapalene inhibits ovarian cancer ES-2 cells g... | 10.1016/j.bioorg.2019.103315 | Glutamic-oxaloacetic transaminase 1 (GOT1) reg... | eng | 2019 | 09 | 26 | 2019 | 10 | 13 | aheadofprint | Adapalene|Drug repurposing|GOT1 inhibitor|Ovar... | ||
7 | 31605903 | Sleep medicine | Obstructive sleep apnea and nocturnal hypoxemi... | 10.1016/j.sleep.2019.05.011 | To identify a link between sleep disordered br... | eng | 2019 | 06 | 06 | 2019 | 10 | 13 | aheadofprint | Home sleep apnea testing|Lung cancer|Lung canc... | ||
8 | 31605879 | Journal of pharmaceutical and biomedical analysis | Metabolic profiling of seminal plasma from ter... | 10.1016/j.jpba.2019.112903 | Teratozoospermia is one of conditions that can... | eng | 2019 | 10 | 03 | 2019 | 10 | 13 | aheadofprint | Human seminal plasma|Male infertility|Metabolo... | ||
9 | 31605873 | European journal of medicinal chemistry | Discovery of potent ureido tetrahydrocarbazole... | 10.1016/j.ejmech.2019.111741 | Tumor-associated macrophages (TAMs) are one of... | eng | 2019 | 09 | 28 | 2019 | 10 | 13 | aheadofprint | Cancer treatments|Repolarization|Tumor-associa... |
# author article
df_author = pd.DataFrame(authorArticleDics)
df_author.head(10)
authorId | PMID | name | identifier | identifierSource | |
---|---|---|---|---|---|
0 | e8d63b09-92dc-471a-a6d2-333e2b637d93 | 31606007 | Manuel Gentiluomo | ||
1 | e825685e-15ce-4498-843b-bcbbfd593a78 | 31606007 | Ye Lu | ||
2 | 47bde920-3b23-4399-b03d-34a9addab6bf | 31606007 | Federico Canzian | ||
3 | c0f8fb31-7b11-41a8-a7f4-bd14af72b7f6 | 31606007 | Daniele Campa | ||
4 | 1f85f904-70de-41b9-8829-6aba22695f90 | 31606005 | Susanne W Gibbons | ||
5 | 8b3e5cc9-2c24-4c0a-a93a-75faa9d96b09 | 31606005 | Alyson Ross | ||
6 | d292a431-624d-4a8a-8817-d0fbdb682658 | 31606005 | Leslie Wehrlen | ||
7 | 2b1bec9d-c96a-404b-8122-c87be5b73e9f | 31606005 | Stephen Klagholz | ||
8 | 4e788cb0-b5c0-4b8c-9de1-f4cfc4f48015 | 31606005 | Margaret Bevans | ||
9 | e7d7838d-407a-42f2-8568-93c2118763d5 | 31605953 | Yi Lu |
# author affiliation
df_affiliation = pd.DataFrame(authorAffiliationDics)
df_affiliation.head(10)
authorId | affiliation | |
---|---|---|
0 | e8d63b09-92dc-471a-a6d2-333e2b637d93 | Department of Biology, University of Pisa, Pis... |
1 | e825685e-15ce-4498-843b-bcbbfd593a78 | Genomic Epidemiology Group, German Cancer Rese... |
2 | 47bde920-3b23-4399-b03d-34a9addab6bf | Genomic Epidemiology Group, German Cancer Rese... |
3 | 1f85f904-70de-41b9-8829-6aba22695f90 | Uniformed Services University of the Health Sc... |
4 | 8b3e5cc9-2c24-4c0a-a93a-75faa9d96b09 | National Institutes of Health, Clinical Center... |
5 | d292a431-624d-4a8a-8817-d0fbdb682658 | National Institutes of Health, Clinical Center... |
6 | 2b1bec9d-c96a-404b-8122-c87be5b73e9f | National Institutes of Health, Clinical Center... |
7 | 4e788cb0-b5c0-4b8c-9de1-f4cfc4f48015 | National Institutes of Health, Clinical Center... |
8 | e7d7838d-407a-42f2-8568-93c2118763d5 | Department of Nutrition, Institute of Cancer R... |
9 | b0bf4f73-ee0b-4631-8ffe-d61d2f2e14e2 | Department of Clinical Lab, the 92nd Hospital ... |
df_article.to_csv('pubmed_article.csv')
df_author.to_csv('pubmed_author.csv')
df_affiliation.to_csv('pubmed_affiliation.csv')
Reload the CSV so that you can resume the session at any time.
# reload
df_article = pd.read_csv('pubmed_article.csv', index_col=0)
df_author = pd.read_csv('pubmed_author.csv', index_col=0)
df_affiliation = pd.read_csv('pubmed_affiliation.csv', index_col=0)
/Users/tatsuya.takahashi/anaconda3/lib/python3.7/site-packages/numpy/lib/arraysetops.py:569: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
print('number of article: ', len(df_article))
number of article: 337416
# Categorical Feature
for catCol in ['Language', 'Status']:
fig = px.bar(df_article[catCol].value_counts().reset_index(), x='index', y=catCol, height=400, width=800, title="{}'s unique count".format(catCol), labels={catCol: 'Count', 'index': catCol})
fig.show()
# concat
# df_article['ArticlePublishDate'] = df_article['Year_A'].fillna(0).astype(int).astype(str).str.zfill(4) + '-' + df_article['Month_A'].fillna(0).astype(int).astype(str).str.zfill(2) + '-' + df_article['Day_A'].fillna(0).astype(int).astype(str).str.zfill(2)
df_article['ArticlePublishDate'] = df_article['Year_A'].fillna(0).astype(int).astype(str).str.zfill(4) + '-' + df_article['Month_A'].fillna(0).astype(int).astype(str).str.zfill(2)
df_article['PubMedPublishDate'] = df_article['Year_PM'].fillna(0).astype(int).astype(str).str.zfill(4) + '-' + df_article['Month_PM'].fillna(0).astype(int).astype(str).str.zfill(2)
for catCol in ['ArticlePublishDate', 'PubMedPublishDate']:
fig = px.line(df_article[df_article[catCol] != '0000-00'][catCol].value_counts().reset_index().sort_values('index'), x='index', y=catCol, height=600, width=1200, title="{}'s distribution".format(catCol), labels={catCol: 'Publish Count', 'index': catCol})
fig.show()
df_article[df_article['Language'] != 'eng'].head(5)
PMID | JournalTitle | Title | doi | Abstract | Language | Year_A | Month_A | Day_A | Year_PM | Month_PM | Day_PM | Status | MeSH | MeSH_UI | Keyword | ArticlePublishDate | PubMedPublishDate | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
208 | 31604575 | Annales de pathologie | [Guidelines for the macroscopic management of ... | 10.1016/j.annpat.2019.05.008 | Gross examination is an essential step for pat... | fre | 2019.0 | 10.0 | 8.0 | 2019 | 10 | 13 | aheadofprint | NaN | NaN | Cancer pulmonaire|Guidelines|Lung cancer|Macro... | 2019-10 | 2019-10 |
209 | 31604570 | Bulletin du cancer | [Equal access to patient education in oncology... | 10.1016/j.bulcan.2019.08.015 | NaN | fre | 2019.0 | 10.0 | 8.0 | 2019 | 10 | 13 | aheadofprint | NaN | NaN | Cancer|Chronic disease|Health care inequalitie... | 2019-10 | 2019-10 |
403 | 31602954 | Zhongguo Zhong yao za zhi = Zhongguo zhongyao ... | [Regulatory effects of glabridin and quercetin... | 10.19540/j.cnki.cjcmm.20190505.401 | It is reported that energy metabolism is the c... | chi | NaN | NaN | NaN | 2019 | 10 | 12 | ppublish | NaN | NaN | breast cancer cell|energy metabolism|glabridin... | 0000-00 | 2019-10 |
404 | 31602944 | Zhongguo Zhong yao za zhi = Zhongguo zhongyao ... | [A landscape of transcriptome analysis of thre... | 10.19540/j.cnki.cjcmm.20190701.112 | Polyporus umbellatus,a traditional Chinese pre... | chi | NaN | NaN | NaN | 2019 | 10 | 12 | ppublish | NaN | NaN | effective content|growth|sclerotia of Polyporu... | 0000-00 | 2019-10 |
405 | 31602910 | Zhongguo Zhong yao za zhi = Zhongguo zhongyao ... | [Pharmacodynamic effect and virulent effect of... | 10.19540/j.cnki.cjcmm.20181119.001 | To investigate the pharmacodynamic effect and ... | chi | NaN | NaN | NaN | 2019 | 10 | 12 | ppublish | NaN | NaN | ADME/T|Tripterygium wilfordii|network pharmaco... | 0000-00 | 2019-10 |
# False: not nan, True: is nan, values are percent
pd.merge(df_article, df_author, on='PMID', how='left').isnull().apply(lambda col: col.value_counts(), axis=0).fillna(0).astype(np.float).apply(lambda col: col/col.sum(), axis=0)
PMID | JournalTitle | Title | doi | Abstract | Language | Year_A | Month_A | Day_A | Year_PM | ... | Status | MeSH | MeSH_UI | Keyword | ArticlePublishDate | PubMedPublishDate | authorId | name | identifier | identifierSource | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
False | 1.0 | 1.0 | 0.994961 | 0.977648 | 0.920882 | 1.0 | 0.818336 | 0.818336 | 0.818336 | 1.0 | ... | 1.0 | 0.531469 | 0.531469 | 0.648765 | 1.0 | 1.0 | 0.999396 | 0.999396 | 0.074503 | 0.074503 |
True | 0.0 | 0.0 | 0.005039 | 0.022352 | 0.079118 | 0.0 | 0.181664 | 0.181664 | 0.181664 | 0.0 | ... | 0.0 | 0.468531 | 0.468531 | 0.351235 | 0.0 | 0.0 | 0.000604 | 0.000604 | 0.925497 | 0.925497 |
2 rows × 22 columns
for catCol in ['authorId']:
fig = px.bar(df_author.groupby('PMID', as_index=False).count()[catCol].value_counts().reset_index(), x='index', y=catCol, height=600, width=1600, title="How many authors in each articles?".format(catCol), labels={catCol: 'Count', 'index': catCol})
fig.show()
# False: not nan, True: is nan, values are percent
pd.DataFrame(pd.DataFrame(df_article['MeSH'].fillna('').astype(str) + df_article['Keyword'].fillna('').astype(str))[0] == '').apply(lambda col: col.value_counts(), axis=0).fillna(0).astype(np.float).apply(lambda col: col/col.sum(), axis=0)
0 | |
---|---|
False | 0.861903 |
True | 0.138097 |
df_article['allText'] = df_article['Title'].fillna('') + df_article['Abstract'].fillna('') + df_article['MeSH'].fillna('') + df_article['Keyword'].fillna('')
tfidf = TfidfVectorizer(
min_df = 5,
max_df = 0.95,
max_features = 8000,
stop_words = 'english'
)
tfidf.fit(df_article.allText)
text = tfidf.fit_transform(df_article.allText)
"""
Finding Optimal Clusters¶
https://www.kaggle.com/jbencina/clustering-documents-with-tfidf-and-kmeans
"""
def find_optimal_clusters(data, max_k):
iters = range(10, max_k+1, 10)
sse = []
for k in iters:
sse.append(MiniBatchKMeans(n_clusters=k, init_size=1024, batch_size=2048, random_state=20).fit(data).inertia_)
print('Fit {} clusters'.format(k))
f, ax = plt.subplots(1, 1)
ax.plot(iters, sse, marker='o')
ax.set_xlabel('Cluster Centers')
ax.set_xticks(iters)
ax.set_xticklabels(iters)
ax.set_ylabel('SSE')
ax.set_title('SSE by Cluster Center Plot')
find_optimal_clusters(text, 100)
Fit 10 clusters Fit 20 clusters Fit 30 clusters Fit 40 clusters Fit 50 clusters Fit 60 clusters Fit 70 clusters Fit 80 clusters Fit 90 clusters Fit 100 clusters
# Clustring
clusters = MiniBatchKMeans(n_clusters=80, init_size=1024, batch_size=2048, random_state=20).fit_predict(text)
print(text.shape)
print(len(clusters))
(337416, 8000) 337416
# random sampling size
RANDOM_SAMPLING_SIZE = 3000
# random sampling
random_idx = np.random.choice(range(text.shape[0]), size=RANDOM_SAMPLING_SIZE, replace=False)
# t-sne(with random sampling pca)
tsne = TSNE(random_state=RANDOM_STATE).fit_transform(PCA(n_components=50, random_state=RANDOM_STATE).fit_transform(text[random_idx,:].todense()))
# random sampling df
df_article_tsne = df_article.iloc[random_idx]
# horizontal concat
df_article_tsne = df_article.iloc[random_idx].copy()
df_article_tsne['tsne_x'] = tsne[:, 0]
df_article_tsne['tsne_y'] = tsne[:, 1]
df_article_tsne['cluster'] = clusters[random_idx]
df_article_tsne.head()
PMID | JournalTitle | Title | doi | Abstract | Language | Year_A | Month_A | Day_A | Year_PM | ... | Status | MeSH | MeSH_UI | Keyword | ArticlePublishDate | PubMedPublishDate | allText | tsne_x | tsne_y | cluster | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
32085 | 31354359 | Cancer management and research | Sinonasal/nasopharyngeal pleomorphic adenoma a... | 10.2147/CMAR.S198942 | NaN | eng | 2019.0 | 6.0 | 17.0 | 2019 | ... | epublish | NaN | NaN | carcinoma ex- pleomorphic adenoma|endoscopic|n... | 2019-06 | 2019-07 | Sinonasal/nasopharyngeal pleomorphic adenoma a... | -9.454226 | 26.023804 | 53 |
116782 | 30690027 | Experimental cell research | Notch1 inhibition enhances DNA damage induced ... | 10.1016/j.yexcr.2019.01.014 | The expression of Notch1 plays an important ro... | eng | 2019.0 | 1.0 | 26.0 | 2019 | ... | ppublish | NaN | NaN | ATM|Apoptosis|Cervical cancer|Cisplatin|DNA da... | 2019-01 | 2019-01 | Notch1 inhibition enhances DNA damage induced ... | -48.622681 | -6.096260 | 70 |
35940 | 31323930 | Vaccines | From Vaccine Vector to Oncomodulation: Underst... | 10.3390/vaccines7030062 | Cytomegalovirus (CMV) is a herpesvirus that es... | eng | 2019.0 | 7.0 | 9.0 | 2019 | ... | epublish | NaN | NaN | anti-tumor immunity|cancer vaccines|cytomegalo... | 2019-07 | 2019-07 | From Vaccine Vector to Oncomodulation: Underst... | -3.073254 | -9.257894 | 53 |
253401 | 29673046 | Diabetes/metabolism research and reviews | Newly diagnosed type 2 diabetes may serve as a... | 10.1002/dmrr.3018 | Pancreatic cancer has an extremely highly case... | eng | 2018.0 | 6.0 | 17.0 | 2018 | ... | ppublish | Adult|Biomarkers, Tumor|Diabetes Mellitus, Typ... | D000328|D014408|D003924|D018450|D055088|D00526... | early detection|newly diagnosed diabetes|pancr... | 2018-06 | 2018-04 | Newly diagnosed type 2 diabetes may serve as a... | 37.316956 | -39.627686 | 67 |
32094 | 31354350 | Cancer management and research | Bioinformatics analysis of dysregulated microR... | 10.2147/CMAR.S201335 | NaN | eng | 2019.0 | 6.0 | 12.0 | 2019 | ... | epublish | NaN | NaN | breast cancer|chemoresistance|docetaxel|exosom... | 2019-06 | 2019-07 | Bioinformatics analysis of dysregulated microR... | 50.381680 | 3.608618 | 10 |
5 rows × 22 columns
# scatter visualize
fig = px.scatter(
df_article_tsne,
x="tsne_x",
y="tsne_y",
color="cluster",
height=1200,
# size='petal_length',
color_continuous_scale=px.colors.sequential.Plasma,
hover_data=['Title', 'PMID']
)
fig.update_layout(
showlegend=False
)
fig.show()
def get_top_keywords(data, clusters, labels, n_terms):
df = pd.DataFrame(data.todense()).groupby(clusters).mean()
clusterTexts = []
for i,r in df.iterrows():
top_keywords = ','.join([labels[t] for t in np.argsort(r)[-n_terms:]])
clusterTexts.append(top_keywords)
# print('\nCluster {}'.format(i))
# print(top_keywords)
return clusterTexts
clusterTexts = get_top_keywords(text, clusters, tfidf.get_feature_names(), 10)
df_article['cluster'] = clusters
df_cluster = pd.DataFrame(df_article.groupby('cluster', as_index=False).count().sort_values('cluster')['PMID'].values, columns=['num_articles'])
df_cluster['keywords'] = clusterTexts
df_cluster.sort_values('num_articles')
num_articles | keywords | |
---|---|---|
48 | 1 | cell,adhesion,metastatic,integrin,sponge,parag... |
51 | 1 | prospective,limb,shoulder,circumference,01,lym... |
49 | 1 | reaching,mtx,hd,progression,pcnsl,patients,yea... |
31 | 2 | persons,cancer,malignant,history,cancers,disea... |
50 | 42 | tumour,nanomedicine,regulates,reproducibility,... |
65 | 530 | cells,ferritin,cancer,nanoparticles,ferroptosi... |
62 | 547 | malignant,diagnosis,rare,case,tumors,ovarian,t... |
60 | 896 | apparent,adc,coefficient,dwi,mri,magnetic,reso... |
59 | 915 | therapy,adoptive,cd19,receptor,immunotherapy,c... |
33 | 929 | factors,heparin,cancer,anticoagulants,patients... |
61 | 965 | body,smooth,atrophy,cancer,wasting,mass,cachex... |
40 | 1054 | eus,cytology,endoscopic,fna,ultrasound,guided,... |
8 | 1088 | metastasis,tumor,cells,proliferation,cell,mir,... |
42 | 1218 | recurrence,robotic,assisted,cancer,rp,robot,pr... |
28 | 1331 | neoplasms,tumor,gi,tract,imatinib,gists,tumors... |
55 | 1400 | cell,acetylation,hdac,lysine,inhibitors,methyl... |
71 | 1432 | genes,variants,genetic,cancer,germline,breast,... |
74 | 1452 | tumor,proliferation,expression,cancer,cells,ce... |
57 | 1460 | therapy,adt,receptor,cancer,resistant,deprivat... |
66 | 1482 | net,aged,somatostatin,tumor,carcinoma,neoplasm... |
7 | 1643 | patients,growth,erbb,epidermal,cancer,receptor... |
38 | 1783 | proteins,mtor,protein,autophagic,induced,cance... |
69 | 1876 | advanced,response,locally,breast,cancer,chemor... |
56 | 1890 | aged,bone,sts,kaposi,synovial,sarcomas,ewing,t... |
16 | 1904 | cancer,snps,susceptibility,single,risk,associa... |
47 | 1919 | angiogenic,cell,tumor,cells,factor,growth,vegf... |
32 | 2018 | cells,dexamethasone,cell,bone,lenalidomide,pat... |
18 | 2032 | oncology,molecular,genomic,clinical,cancer,seq... |
11 | 2033 | growth,non,receptor,kinase,mutation,small,nscl... |
68 | 2079 | neoplasms,patients,stage,colorectal,tumor,cell... |
... | ... | ... |
23 | 3644 | iodine,follicular,thyroidectomy,differentiated... |
63 | 3726 | tumor,mouth,aged,cancer,scc,oscc,cell,oral,car... |
27 | 3760 | tumor,aged,patients,cell,cutaneous,uveal,metas... |
20 | 4087 | cancer,tumor,cells,imaging,photodynamic,nps,go... |
34 | 4114 | rituximab,aged,follicular,patients,dlbcl,large... |
30 | 4312 | eoc,female,neoplasms,tumor,chemotherapy,cell,s... |
78 | 4466 | adenocarcinoma,aged,endoscopic,patients,helico... |
13 | 4592 | stereotactic,cancer,treatment,dose,planning,in... |
67 | 4810 | survival,patients,neoplasms,tumor,pancreas,ade... |
41 | 4848 | image,mr,aged,neoplasms,prostate,contrast,mri,... |
70 | 4898 | tumor,genome,cells,cancer,cell,replication,dam... |
35 | 4937 | services,oncology,quality,life,patients,patien... |
4 | 5092 | synthesis,molecular,drug,anticancer,agents,cel... |
37 | 5232 | microrna,micrornas,cells,cancer,proliferation,... |
26 | 5302 | inhibitors,microenvironment,immunity,cell,canc... |
14 | 5363 | survival,expression,tumor,hepatitis,patients,s... |
19 | 5724 | doxorubicin,systems,cells,dox,tumor,release,ca... |
64 | 5759 | cells,patients,lymphocytic,cell,chronic,lympho... |
21 | 5889 | biopsy,psa,castration,specific,men,antigen,pca... |
39 | 6651 | metastatic,risk,aged,expression,tumor,neoplasm... |
12 | 7341 | minimally,complications,procedures,postoperati... |
1 | 7565 | genome,rnas,regulation,cell,analysis,cancer,ge... |
3 | 8226 | cells,molecular,domain,signaling,inhibitors,ce... |
2 | 9760 | aged,carcinoma,adenocarcinoma,patients,nsclc,c... |
73 | 11366 | survival,factors,male,female,risk,middle,adult... |
17 | 11692 | cells,mitochondrial,oxidative,inflammatory,can... |
10 | 12676 | aged,mastectomy,negative,neoplasms,patients,ri... |
36 | 16010 | patient,medical,risk,survivors,clinical,patien... |
9 | 18508 | human,mice,stem,proliferation,expression,apopt... |
53 | 42627 | study,treatment,diagnosis,disease,neoplasms,tu... |
80 rows × 2 columns