Searching PubMed with Biopython

search_biopython.py

# 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 = '[email protected]'
    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 = '[email protected]'
    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']))

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!

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=(',', ':')))

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

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!

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?

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 = '[email protected]'
    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 = '[email protected]'
    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()