PubMed提取文章详细信息到Daframe
这是代码。
import pandas as pd
from pymed import PubMed
import numpy as np
pubmed = PubMed(tool="PubMedSearcher", email="[email protected]")
## PUT YOUR SEARCH TERM HERE ##
search_term = 'Charlie Brown'
results = pubmed.query(search_term, max_results=100000)
articleList = []
articleInfo = []
for article in results:
# Print the type of object we've found (can be either PubMedBookArticle or PubMedArticle).
# We need to convert it to dictionary with available function
articleDict = article.toDict()
articleList.append(articleDict)
# Generate list of dict records which will hold all article details that could be fetch from PUBMED API
for article in articleList:
#Sometimes article['pubmed_id'] contains list separated with comma - take first pubmedId in that list - thats article pubmedId
pubmedId = article['pubmed_id'].partition('\n')[0]
# Append article info to dictionary
articleInfo.append({u'pubmed_id':pubmedId,
u'publication_date':article['publication_date'],
u'authors':article['authors']})
df=pd.json_normalize(articleInfo)
运行此代码将获取三列，PubMed_ID，publication_date和作者 。
有没有办法可以不介意作者列并保留其他两个列？非常感谢。
Here is the code.
import pandas as pd
from pymed import PubMed
import numpy as np
pubmed = PubMed(tool="PubMedSearcher", email="[email protected]")
## PUT YOUR SEARCH TERM HERE ##
search_term = 'Charlie Brown'
results = pubmed.query(search_term, max_results=100000)
articleList = []
articleInfo = []
for article in results:
# Print the type of object we've found (can be either PubMedBookArticle or PubMedArticle).
# We need to convert it to dictionary with available function
articleDict = article.toDict()
articleList.append(articleDict)
# Generate list of dict records which will hold all article details that could be fetch from PUBMED API
for article in articleList:
#Sometimes article['pubmed_id'] contains list separated with comma - take first pubmedId in that list - thats article pubmedId
pubmedId = article['pubmed_id'].partition('\n')[0]
# Append article info to dictionary
articleInfo.append({u'pubmed_id':pubmedId,
u'publication_date':article['publication_date'],
u'authors':article['authors']})
df=pd.json_normalize(articleInfo)
Running this code would fetch three columns, pubmed_id, publication_date and authors
.
Is there a way to unnest the authors column and keep the other two columns? Thanks so much in advance.
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如果您想不愿意，那么您必须定义一些策略。例如，您可以使用
LastName，FirstName将每个作者用;：输出：输出：
If you want to unnest then, you have to define some strategy. For example, you can join the authors with
lastname, firstnamesplitting each author with;:Output: