python - 使用 Entrez 解析来自 PubMed 的出版数据的问题

Question

我正在尝试使用 Entrez 将发布数据导入数据库。搜索部分工作正常，但是当我尝试解析时:

from Bio import Entrez

def create_publication(pmid):

    handle = Entrez.efetch("pubmed", id=pmid, retmode="xml")
    records = Entrez.parse(handle)
    item_data = records.next()
    handle.close()

...我收到以下错误:

File "/venv/lib/python2.7/site-packages/Bio/Entrez/Parser.py", line 296, in parse raise ValueError("The XML file does not represent a list. Please use Entrez.read instead of Entrez.parse") ValueError: The XML file does not represent a list. Please use Entrez.read instead of Entrez.parse

这段代码在几天前一直有效。知道这里可能出了什么问题吗？

此外，查看源代码 ( http://biopython.org/DIST/docs/api/Bio.Entrez-pysrc.html ) 并尝试按照列出的示例进行操作，也会出现相同的错误:

from Bio import Entrez 
Entrez.email = "Your.Name.Here@example.org"
handle = Entrez.efetch("pubmed", id="19304878,14630660", retmode="xml")    
records = Entrez.parse(handle) 
for record in records: 
    print(record['MedlineCitation']['Article']['ArticleTitle']) 
handle.close()

Answer 1

问题，如其他评论和 GitHub Issue 中所述, 是由 NCBI Entrez Utilities Developers 故意更改引起的。如 Jhird 在本期中所述，您可以将代码更改为以下内容:

from Bio import Entrez 
Entrez.email = "Your.Name.Here@example.org"
handle = Entrez.efetch("pubmed", id="19304878,14630660", retmode="xml")  

records = Entrez.read(handle)      # Difference here
records = records['PubmedArticle'] # New line here  

for record in records: 
    print(record['MedlineCitation']['Article']['ArticleTitle']) 
handle.close()