目录
E-utilities的介绍可以参考此处。
第一种方法：构造url使用Entrez数据库检索
通过Python利用E-utilities来搜索和下载文献，一种方式是构造url，如：
#载入需要用到的包
import requests
import json
try:
import xml.etree.cElementTree as ET
except ImportError:
import xml.etree.ElementTree as ET
#构造检索式，获取相应检索结果的UID。首先指定检索数据库
db = "pubmed"
#在此处构造检索式，注意检索式的构造规则<https://www.ncbi.nlm.nih.gov/books/NBK25497/>
query = "Hsuan-Yu Chen"
#Entrez数据库公用的base url
base = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/'
#url参数可查看：<https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch>
url = base + "esearch.fcgi?db=" + db + "&term=" + query + "&retmode=json"+ "&reldate=360&datetype=pdat" + "&retmax=100" + "&usehistory=y"
#获取检索结果的UID列表
re = requests.get(url)
result = re.text
data = json.loads(result)
idlist = data["esearchresult"]["idlist"] #UID list
string = ""
number = len(idlist)
lastone = idlist[number - 1]
for item in idlist:
if item == lastone:
string = string + item
else:
string = string + item + ","
通过这种方式获得检索结果的UID列表后，再用UID构造url进行精确检索，并获取检索结果的题目、摘要等信息。这部分内容参考自：使用python來調用pubmed API快速整理文獻 – 我們的基因體時代 Our Generation。
第二种方法：使用Biopython包的Entrez模块
参考《第9章 访问NCBI Entrez数据库 — Biopython-cn 0.1 文档》及Chapter 12 Accessing NCBI’s Entrez databases。这种方法首先需要pip install Biopython安装Biopython包；然后需要注册一个pubmed账户，最好再在账户里面创建一个API key。
下面是一个自己尝试的一个例子：
from Bio import Entrez
Entrez.email = "xx@xxx.com" # Replace with your email
Entrez.api_key = "pubmed_APIkey" # Replace with your API key
#构造检索式，获取检索结果的UID列表
db = "pubmed"
query = "oral cancer[Title/Abstract]"
handle = Entrez.esearch(db="pubmed", term=query, retmax=2, retmode="xml", sort="pub_date", usehistory="y")
record = Entrez.read(handle)
id_list = record["IdList"]
#构造一个取回文献相关信息的函数，此处包括题目、发表时间、期刊名称以及摘要
def fetch_article_data(item):
try:
handle = Entrez.efetch(db="pubmed", id=item, retmode="xml")
records = Entrez.read(handle)
article = records['PubmedArticle'][0]
Title = article['MedlineCitation']['Article']['ArticleTitle']
Pubdate = article['MedlineCitation']['Article']['Journal']['JournalIssue']['PubDate']
JournalTitle = article['MedlineCitation']['Article']['Journal']['Title']
try:
Abstract = " ".join(article['MedlineCitation']['Article']['Abstract']['AbstractText'])
except KeyError:
Abstract = "No Abstract Found"
return Title, Abstract, Pubdate, Journatitle
except Exception as e:
print(f"Error: {e}")
return "", "",
#利用UID获取文献
totalnumber = len(id_list)
results = []
number = 0
for item in id_list:
number = number + 1
print(f"第{number}/{totalnumber}条 | Processing: {item}")
Title, Abstract, Pubdate, Journatitle = fetch_article_data(item)
sample = {"PMID":item, "PubDate and journal title":f"{Pubdate['Month']}, {Pubdate['Year']}. {JournalTitle}", "Title": Title, "Abstract":Abstract}
results.append(sample)
print(results) #最终结果是UID中所有文献信息的列表
方法二和方法一相比，构造检索式更简单，而且通过API key可以获得更高的查询频率，同时会按照pubmed数据库的要求对查询频率自动进行限制。
通过方法二取回的records是一个json格式的文件。
这是这一文件的内容，可以拷贝后测试获取相应内容：
{‘PubmedArticle’: [{‘MedlineCitation’: DictElement({‘OtherID’: [], ‘OtherAbstract’: [], ‘InvestigatorList’: [], ‘CitationSubset’: [‘IM’], ‘SpaceFlightMission’: [], ‘GeneralNote’: [], ‘KeywordList’: [ListElement([StringElement(‘allogeneic stem cell transplant’, attributes={‘MajorTopicYN’: ‘N’}), StringElement(‘fungal’, attributes={‘MajorTopicYN’: ‘N’}), StringElement(‘hematology’, attributes={‘MajorTopicYN’: ‘N’}), StringElement(‘invasive’, attributes={‘MajorTopicYN’: ‘N’}), StringElement(‘mold’, attributes={‘MajorTopicYN’: ‘N’}), StringElement(‘prevention’, attributes={‘MajorTopicYN’: ‘N’}), StringElement(‘prophylaxis’, attributes={‘MajorTopicYN’: ‘N’})], attributes={‘Owner’: ‘NOTNLM’})], ‘PMID’: StringElement(‘37988269’, attributes={‘Version’: ‘1’}), ‘DateCompleted’: {‘Year’: ‘2023’, ‘Month’: ’12’, ‘Day’: ’11’}, ‘DateRevised’: {‘Year’: ‘2023’, ‘Month’: ’12’, ‘Day’: ’11’}, ‘Article’: DictElement({‘ArticleDate’: [DictElement({‘Year’: ‘2023’, ‘Month’: ’11’, ‘Day’: ’21’}, attributes={‘DateType’: ‘Electronic’})], ‘ELocationID’: [StringElement(‘10.1111/tid.14197’, attributes={‘EIdType’: ‘doi’, ‘ValidYN’: ‘Y’})], ‘Language’: [‘eng’], ‘Journal’: {‘ISSN’: StringElement(‘1399-3062’, attributes={‘IssnType’: ‘Electronic’}), ‘JournalIssue’: DictElement({‘Volume’: ’25 Suppl 1′, ‘PubDate’: {‘Year’: ‘2023’, ‘Month’: ‘Nov’}}, attributes={‘CitedMedium’: ‘Internet’}), ‘Title’: ‘Transplant infectious disease : an official journal of the Transplantation Society’, ‘ISOAbbreviation’: ‘Transpl Infect Dis’}, ‘ArticleTitle’: ‘Approach to diagnostic evaluation and prevention of invasive fungal disease in patients prior to allogeneic hematopoietic stem cell transplant.’, ‘Pagination’: {‘StartPage’: ‘e14197’, ‘MedlinePgn’: ‘e14197’}, ‘Abstract’: {‘AbstractText’: ["In recent years, advancements in the treatment landscape for hematological malignancies, such as acute myeloid leukemia and acute lymphoblastic leukemia, have significantly improved disease prognosis and overall survival. However, the treatment landscape is changing and the emergence of targeted oral therapies and immune-based treatments has brought forth new challenges in evaluating and preventing invasive fungal diseases (IFDs). IFD disproportionately affects immunocompromised hosts, particularly those undergoing therapy for acute leukemia and allogeneic hematopoietic stem cell transplant. This review aims to provide a comprehensive overview of the pretransplant workup, identification, and prevention of IFD in patients with hematological malignancy. The pretransplant period offers a critical window to assess each patient’s risk factors and implement appropriate prophylactic measures. Risk assessment includes evaluation of disease, host, prior treatments, and environmental factors, allowing a dynamic evaluation that considers disease progression and treatment course. Diagnostic screening, involving various biomarkers and radiological modalities, plays a crucial role in early detection of IFD. Antifungal prophylaxis choice is based on available evidence as well as individual risk assessment, potential for drug-drug interactions, toxicity, and patient adherence. Therapeutic drug monitoring ensures effective antifungal stewardship and optimal treatment. Patient education and counselling are vital in minimizing environmental exposures to fungal pathogens and promoting medication adherence. A well-structured and individualized approach, encompassing risk assessment, prophylaxis, surveillance, and patient education, is essential for effectively preventing IFD in hematological malignancies, ultimately leading to improved patient outcomes and overall survival."], ‘CopyrightInformation’: ‘© 2023 Wiley Periodicals LLC.’}, ‘AuthorList’: ListElement([DictElement({‘AffiliationInfo’: [{‘Identifier’: [], ‘Affiliation’: ‘Victorian Infectious Diseases Service, Royal Melbourne Hospital, Parkville, Victoria, Australia.’}], ‘Identifier’: [StringElement(‘0000-0002-0293-3221’, attributes={‘Source’: ‘ORCID’})], ‘LastName’: "O’Keeffe", ‘ForeName’: ‘Jessica C’, ‘Initials’: ‘JC’}, attributes={‘ValidYN’: ‘Y’}), DictElement({‘AffiliationInfo’: [{‘Identifier’: [], ‘Affiliation’: ‘Department of Infectious Diseases, Peter MacCallum Cancer Centre, Parkville, Victoria, Australia.’}, {‘Identifier’: [], ‘Affiliation’: ‘Department of Pharmacy, Peter MacCallum Cancer Centre, Parkville, Victoria, Australia.’}], ‘Identifier’: [StringElement(‘0009-0009-5264-2447’, attributes={‘Source’: ‘ORCID’})], ‘LastName’: ‘Singh’, ‘ForeName’: ‘Nikhil’, ‘Initials’: ‘N’}, attributes={‘ValidYN’: ‘Y’}), DictElement({‘AffiliationInfo’: [{‘Identifier’: [], ‘Affiliation’: ‘Victorian Infectious Diseases Service, Royal Melbourne Hospital, Parkville, Victoria, Australia.’}, {‘Identifier’: [], ‘Affiliation’: ‘Department of Infectious Diseases, Peter MacCallum Cancer Centre, Parkville, Victoria, Australia.’}, {‘Identifier’: [], ‘Affiliation’: ‘Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.’}], ‘Identifier’: [StringElement(‘0000-0002-8443-314X’, attributes={‘Source’: ‘ORCID’})], ‘LastName’: ‘Slavin’, ‘ForeName’: ‘Monica A’, ‘Initials’: ‘MA’}, attributes={‘ValidYN’: ‘Y’})], attributes={‘CompleteYN’: ‘Y’}), ‘PublicationTypeList’: [StringElement(‘Journal Article’, attributes={‘UI’: ‘D016428’}), StringElement(‘Review’, attributes={‘UI’: ‘D016454’})]}, attributes={‘PubModel’: ‘Print-Electronic’}), ‘MedlineJournalInfo’: {‘Country’: ‘Denmark’, ‘MedlineTA’: ‘Transpl Infect Dis’, ‘NlmUniqueID’: ‘100883688’, ‘ISSNLinking’: ‘1398-2273’}, ‘ChemicalList’: [{‘RegistryNumber’: ‘0’, ‘NameOfSubstance’: StringElement(‘Antifungal Agents’, attributes={‘UI’: ‘D000935’})}], ‘MeshHeadingList’: [{‘QualifierName’: [], ‘DescriptorName’: StringElement(‘Humans’, attributes={‘UI’: ‘D006801’, ‘MajorTopicYN’: ‘N’})}, {‘QualifierName’: [StringElement(‘therapeutic use’, attributes={‘UI’: ‘Q000627’, ‘MajorTopicYN’: ‘N’})], ‘DescriptorName’: StringElement(‘Antifungal Agents’, attributes={‘UI’: ‘D000935’, ‘MajorTopicYN’: ‘N’})}, {‘QualifierName’: [StringElement(‘drug therapy’, attributes={‘UI’: ‘Q000188’, ‘MajorTopicYN’: ‘N’})], ‘DescriptorName’: StringElement(‘Mycoses’, attributes={‘UI’: ‘D009181’, ‘MajorTopicYN’: ‘Y’})}, {‘QualifierName’: [StringElement(‘diagnosis’, attributes={‘UI’: ‘Q000175’, ‘MajorTopicYN’: ‘N’}), StringElement(‘drug therapy’, attributes={‘UI’: ‘Q000188’, ‘MajorTopicYN’: ‘N’}), StringElement(‘prevention & control’, attributes={‘UI’: ‘Q000517’, ‘MajorTopicYN’: ‘N’})], ‘DescriptorName’: StringElement(‘Invasive Fungal Infections’, attributes={‘UI’: ‘D000072742’, ‘MajorTopicYN’: ‘Y’})}, {‘QualifierName’: [StringElement(‘adverse effects’, attributes={‘UI’: ‘Q000009’, ‘MajorTopicYN’: ‘N’})], ‘DescriptorName’: StringElement(‘Hematopoietic Stem Cell Transplantation’, attributes={‘UI’: ‘D018380’, ‘MajorTopicYN’: ‘Y’})}, {‘QualifierName’: [StringElement(‘complications’, attributes={‘UI’: ‘Q000150’, ‘MajorTopicYN’: ‘N’})], ‘DescriptorName’: StringElement(‘Hematologic Neoplasms’, attributes={‘UI’: ‘D019337’, ‘MajorTopicYN’: ‘Y’})}]}, attributes={‘Status’: ‘MEDLINE’, ‘Owner’: ‘NLM’, ‘IndexingMethod’: ‘Automated’}), ‘PubmedData’: {‘ReferenceList’: [{‘Reference’: [{‘Citation’: ‘Chang CC, Blyth CC, Chen SCA, et\xa0al. 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