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@bonzanini
Last active February 9, 2024 21:44
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Searching PubMed with Biopython
# This code uses Biopython to retrieve lists of articles from pubmed
# you need to install Biopython first.
# If you use Anaconda:
# conda install biopython
# If you use pip/venv:
# pip install biopython
# Full discussion:
# https://marcobonzanini.wordpress.com/2015/01/12/searching-pubmed-with-python/
from Bio import Entrez
def search(query):
Entrez.email = 'your.email@example.com'
handle = Entrez.esearch(db='pubmed',
sort='relevance',
retmax='20',
retmode='xml',
term=query)
results = Entrez.read(handle)
return results
def fetch_details(id_list):
ids = ','.join(id_list)
Entrez.email = 'your.email@example.com'
handle = Entrez.efetch(db='pubmed',
retmode='xml',
id=ids)
results = Entrez.read(handle)
return results
if __name__ == '__main__':
results = search('fever')
id_list = results['IdList']
papers = fetch_details(id_list)
for i, paper in enumerate(papers['PubmedArticle']):
print("{}) {}".format(i+1, paper['MedlineCitation']['Article']['ArticleTitle']))
@hongtao510
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Have you encountered the issue that the server will cut you off after querying ~2000 IDs?

@vyvy3n
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vyvy3n commented Jun 20, 2017

Should the Line 32, 33 be changed into:
for i, paper in enumerate(papers['PubmedArticle']): print("%d) %s" % (i+1, paper['MedlineCitation']['Article']['ArticleTitle']))

@nmagee
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nmagee commented Jun 24, 2017

@ThitherShore is correct - I can verify that suggested fix makes this gist functional.

@lemonysoft
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@hongtao510 we download 100 articles in an infinite loop. We see no blocking info since one week.

@badrul1
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badrul1 commented Sep 17, 2017

Please update code with ThitherShore's comment.

@reiaoki
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reiaoki commented Feb 23, 2018

Whenever there is a "+" sing in the content (for example ArticleTitle or AbstractText), it returns a string only after the "+" sign. Does anyone have a way to get around this?
e.g. The title "The Clinicopathological and Prognostic Implications of FoxP3+ Regulatory T Cells in Patients with Colorectal Cancer: A Meta-Analysis." will return "+ Regulatory T Cells in Patients with Colorectal Cancer: A Meta-Analysis"

@TomazAlexandre
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It looks like the format returned by the efetch method is slightly different now

If you replace papers with papers[‘PubmedArticle’] you should get the list or papers,

@makerspaze
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makerspaze commented Jun 4, 2018

@ThitherShore is correct we should use enumerate(papers['PubmedArticle']) instead of enumerate(papers)

@gunnarklee
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gunnarklee commented Dec 16, 2019

for line 36

print(json.dumps(papers['PubmedArticle'][0], indent=2, separators=(',', ':')))
instead of:
print(json.dumps(papers[0], indent=2, separators=(',', ':')))

@prashantkum7
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I get abstracts and not the full text. Any reason why?

@canthonyscott
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I get abstracts and not the full text. Any reason why?

Pubmed does not contain full texts of papers. Abstracts only

@MLHafizur
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How may I save the result in CSV, with Title and Abstract columns?

@sidewinder02139
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sidewinder02139 commented Dec 3, 2020

Quick question: is there a extra ")" (or missing "(" in line 39?
print("%d) %s" % (i+1, paper['MedlineCitation']['Article']['ArticleTitle']))

#edited for formatting

@sidewinder02139
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sidewinder02139 commented Dec 3, 2020

How may I save the result in CSV, with Title and Abstract columns?

@MLZTazim - I'm in the same boat: learning how to use python to drive json to the result. Good fun!
A hint: https://www.geeksforgeeks.org/json-dumps-in-python/

@bonzanini
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Author

Quick question: is there a extra ")" (or missing "(" in line 39?
print("%d) %s" % (i+1, paper['MedlineCitation']['Article']['ArticleTitle']))

#edited for formatting

@sidewinder02139 the syntax is correct: note the first ")" on that line is part of the output string

@sidewinder02139
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Quick question: is there a extra ")" (or missing "(" in line 39?
print("%d) %s" % (i+1, paper['MedlineCitation']['Article']['ArticleTitle']))
#edited for formatting

@sidewinder02139 the syntax is correct: note the first ")" on that line is part of the output string

DOH! LOL
Have a brilliant weekend and stay healthy!
btw, I love the code. Well done!

@jajkelle
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jajkelle commented Jan 21, 2021

ThitherShore is correct. Your code wont work until you enumerate papers['PubmedArticle']
Thank you for the example, but please change this soon so as not to confuse others.
I spent a while trying to figure out what was wrong.

While were at it the last line doesn't work either for the same reason, should be:
import json
print(json.dumps(papers['PubmedArticle'][0], indent=2, separators=(',', ':')))

@bonzanini
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bonzanini commented Jan 25, 2021

ThitherShore is correct. Your code wont work until you enumerate papers['PubmedArticle']
Thank you for the example, but please change this soon so as not to confuse others.
I spent a while trying to figure out what was wrong.

While were at it the last line doesn't work either for the same reason, should be:
import json
print(json.dumps(papers['PubmedArticle'][0], indent=2, separators=(',', ':')))

@jajkelle Updated (better late than never), thank you all for pointing it out

@echorule
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echorule commented Dec 6, 2022

This is awesome thanks and works pretty well. I'm stuck on trying to get the details of the authors in a succinct way, can anybody help with how to do that? paper['MedlineCitation']['Article']['AuthorList'] isnt right....
Thanks in advance!

@rsgoncalves
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Thanks this is very helpful. Somewhat similar to @echorule, I'm having trouble obtaining the full abstract of a paper as one string. What I get looks like this:

StringElement(' ... ', attributes={'Label': 'BACKGROUND', 'NlmCategory': 'BACKGROUND'}), StringElement(' ... ', attributes={'Label': 'METHODS', 'NlmCategory': 'METHODS'}), StringElement('...' ...)

Is there a more reasonable way to go about this?

@echorule
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echorule commented Jun 21, 2023

Thanks this is very helpful. Somewhat similar to @echorule, I'm having trouble obtaining the full abstract of a paper as one string. What I get looks like this:

StringElement(' ... ', attributes={'Label': 'BACKGROUND', 'NlmCategory': 'BACKGROUND'}), StringElement(' ... ', attributes={'Label': 'METHODS', 'NlmCategory': 'METHODS'}), StringElement('...' ...)

Is there a more reasonable way to go about this?

@rsgoncalves did you manage to resolve this? You can fetch abstract by using: paper['MedlineCitation']['Article']['Abstract']['AbstractText']

So your full code retrieving for author, title and abstract could look something like:


from Bio import Entrez

def search(query):
    Entrez.email = 'your.email@example.com'
    handle = Entrez.esearch(db='pubmed',
                            sort='relevance',
                            retmax='20',
                            retmode='xml',
                            term=query)
    results = Entrez.read(handle)
    return results

def fetch_details(id_list):
    ids = ','.join(id_list)
    Entrez.email = 'your.email@example.com'
    handle = Entrez.efetch(db='pubmed',
                           retmode='xml',
                           id=ids)
    results = Entrez.read(handle)
    return results

def get_abstract(paper):
    abstract = ''
    if 'Abstract' in paper['MedlineCitation']['Article']:
        abstract = paper['MedlineCitation']['Article']['Abstract']['AbstractText']
        if isinstance(abstract, list):
            abstract = ' '.join(abstract)
    return abstract

if __name__ == '__main__':
    results = search('fever')
    id_list = results['IdList']
    papers = fetch_details(id_list)
    for i, paper in enumerate(papers['PubmedArticle']):
        title = paper['MedlineCitation']['Article']['ArticleTitle']
        author_list = paper['MedlineCitation']['Article']['AuthorList']
        authors = ', '.join([author.get('LastName', '') for author in author_list])
        abstract = get_abstract(paper)
        print("{}) Title: {}".format(i+1, title))
        print("   Authors: {}".format(authors))
        print("   Abstract: {}".format(abstract))
        print()

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