Pubmed fetch article details to a daframe-CodePudding

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.

CodePudding user response：

If you want to unnest then, you have to define some strategy. For example, you can join the authors with lastname, firstname splitting each author with ;:

# New column to easily identify how many authors there are in the paper
df['n_authors'] = df['authors'].map(len)

# Unnest authors into a single string using the above-mentioned strategy
df['authors'] = df['authors'].map(lambda authors: ';'.join([f"{author['lastname']}, {author['firstname']}" for author in authors]))

Output:

   pubmed_id publication_date                                            authors  n_authors  
0   35435469       2022-04-19  Easwaran, Raju;Khan, Moin;Sancheti, Parag;Shya...         41  
1   34480858       2021-09-05  Flaxman, Amy;Marchevsky, Natalie G;Jenkin, Dan...         38  
2   30857579       2019-03-13                                     Brown, Charlie          1  
3   28640023       2017-06-24  Thornton, Kevin C;Schwarz, Jennifer J;Gross, A...         12  
4   24195874       2013-11-08  Bicket, Mark C;Gupta, Anita;Brown, Charlie H;C...          4  
5   21741796       2011-07-12  Bird, Jonathan H;Carmont, Michael R;Dhillon, M...          7  
6   21324873       2011-02-18  Cohen, Steven P;Brown, Charlie;Kurihara, Conni...          6  
7   20228712       2010-03-17  Cohen, Steven P;Kapoor, Shruti G;Nguyen, Cuong...          8  
8   20109957       2010-01-30  Cohen, Steven P;Brown, Charlie;Kurihara, Conni...          6  
9   18248779       2008-02-06  Whitaker, Iain S;Duggan, Eileen M;Alloway, Rit...         10  
10  16917639       2006-08-19  Drayton, William;Brown, Charlie;Hillhouse, Karin          3  
11  16282488       2005-11-12  Mao, Hanwen;Lafont, Bernard A P;Igarashi, Tats...          9  
12  14581571       2003-10-29  Moniuszko, Marcin;Brown, Charlie;Pal, Ranajit;...          7  
13  12163382       2002-08-07  Williams, Kenneth;Schwartz, Annette;Corey, Sar...         10