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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']))
@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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