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# 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'])) |
for line 36
print(json.dumps(papers['PubmedArticle'][0], indent=2, separators=(',', ':')))
instead of:
print(json.dumps(papers[0], indent=2, separators=(',', ':')))
I get abstracts and not the full text. Any reason why?
I get abstracts and not the full text. Any reason why?
Pubmed does not contain full texts of papers. Abstracts only
How may I save the result in CSV, with Title and Abstract columns?
Quick question: is there a extra ")" (or missing "(" in line 39?
print("%d) %s" % (i+1, paper['MedlineCitation']['Article']['ArticleTitle']))
#edited for formatting
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/
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
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 = '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()
@ThitherShore is correct we should use
enumerate(papers['PubmedArticle'])
instead ofenumerate(papers)